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Outline of this article: 

I. Catholic Doctrine regarding sex.
II. Catholic Doctrine regarding complicity in the sins of others.
III. Catholic Doctrine regarding obedience.
IV. Catholic Doctrine regarding excommunication.
V. Summary.

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I. Catholic Doctrine regarding sex.

From the Catechism:

http://www.scborromeo.org/ccc/p3s2c2a6.htm

2348 All the baptized are called to chastity. The Christian has "put on Christ,"[135] the model for all chastity. All Christ's faithful are called to lead a chaste life in keeping with their particular states of life. At the moment of his Baptism, the Christian is pledged to lead his affective life in chastity.

2349 "People should cultivate [chastity] in the way that is suited to their state of life. Some profess virginity or consecrated celibacy which enables them to give themselves to God alone with an undivided heart in a remarkable manner. Others live in the way prescribed for all by the moral law, whether they are married or single."[136]   Married people are called to live conjugal chastity; others practice chastity in continence:    There are three forms of the virtue of chastity: the first is that of spouses, the second that of widows, and the third that of virgins.  We do not praise any one of them to the exclusion of the others. . . . This is what makes for the richness of the discipline of the Church. [137]

2351 Lust is disordered desire for or inordinate enjoyment of sexual pleasure. Sexual pleasure is morally disordered when sought for itself, isolated from its procreative and unitive purposes.

2356 Rape is the forcible violation of the sexual intimacy of another person. It does injury to justice and charity. Rape deeply wounds the respect, freedom, and physical and moral integrity to which every person has a right. It causes grave damage that can mark the victim for life. It is always an intrinsically evil act. Graver still is the rape of children committed by parents (incest) or those responsible for the education of the children entrusted to them. 

2357 Homosexuality refers to relations between men or between women who experience an exclusive or predominant sexual attraction toward persons of the same sex. It has taken a great variety of forms through the centuries and in different cultures. Its psychological genesis remains largely unexplained. Basing itself on Sacred Scripture, which presents homosexual acts as acts of grave depravity,[141] tradition has always declared that "homosexual acts are intrinsically disordered."[142] They are contrary to the natural law. They close the sexual act to the gift of life. They do not proceed from a genuine affective and sexual complementarity. Under no circumstances can they be approved. 

2358 The number of men and women who have deep-seated homosexual tendencies is not negligible. This inclination, which is objectively disordered, constitutes for most of them a trial. They must be accepted with respect, compassion, and sensitivity. Every sign of unjust discrimination in their regard should be avoided. These persons are called to fulfill God's will in their lives and, if they are Christians, to unite to the sacrifice of the Lord's Cross the difficulties they may encounter from their condition. 

2359 Homosexual persons are called to chastity. By the virtues of self-mastery that teach them inner freedom, at times by the support of disinterested friendship, by prayer and sacramental grace, they can and should gradually and resolutely approach Christian perfection. 

Notes:

135 Gal 3:27.
136 CDF, Persona humana 11.
137 St. Ambrose, De viduis 4,23:PL 16,255A.
141 Cf. Gen 191-29; Rom 124-27; 1 Cor 6:10; 1 Tim 1:10.
142 CDF, Persona humana 8.

(end quote) 

It should be clear from the above that Catholic Doctrine in no way
endorses priestly pedophilia. 

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II. Catholic Doctrine regarding complicity in the sins of others.

From the Catechism:

http://www.scborromeo.org/ccc/p3s1c1a8.htm

V. THE PROLIFERATION OF SIN

. . .

1868 Sin is a personal act. Moreover, we have a responsibility for the sins committed by others when we cooperate in them:

- by participating directly and voluntarily in them;

- by ordering, advising, praising, or approving them;

- by not disclosing or not hindering them when we have an obligation to do so;

- by protecting evil-doers.

(end quote) 

It should be clear from the above that Catholic Doctrine in no way endorses episcopal cover-ups of priestly pedophilia. 

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III. Catholic Doctrine regarding obedience.

From the Summa Theologica:

http://www.newadvent.org/summa/3104.htm 

Article 3. Whether obedience is the greatest of the virtues? 

. . . obedience deserves praise because it proceeds from charity: for Gregory says (Moral. xxxv) that "obedience should be practiced, not out of servile fear, but from a sense of charity, not through fear of punishment, but through love of justice." Therefore charity is a greater virtue than obedience.I answer that, Just as sin consists in man contemning God and adhering to mutable things, so the merit of a virtuous act consists in man contemning created goods and adhering to God as his end. Now the end is greater than that which is directed to the end. Therefore if a man contemns created goods in order that he may adhere to God, his virtue derives greater praise from his adhering to God than from his contemning earthly things. And so those, namely the theological, virtues whereby he adheres to God in Himself, are greater than the moral virtues, whereby he holds in contempt some earthly thing in order to adhere to God.

Among the moral virtues, the greater the thing which a man contemns that he may adhere to God, the greater the virtue. Now there are three kinds of human goods that man may contemn for God's sake. The lowest of these are external goods, the goods of the body take the middle place, and the highest are the goods of the soul; and among these the chief, in a way, is the will, in so far as, by his will, man makes use of all other goods. Therefore, properly speaking, the virtue of obedience, whereby we contemn our own will for God's sake, is more praiseworthy than the other moral virtues, which contemn other goods for the sake of God.

Hence Gregory says (Moral. xxxv) that "obedience is rightly preferred to sacrifices, because by sacrifices another's body is slain whereas by obedience we slay our own will." Wherefore even any other acts of virtue are meritorious before God through being performed out of obedience to God's will. For were one to suffer even martyrdom, or to give all one's goods to the poor, unless one directed these things to the fulfilment of the divine will, which pertains directly to obedience, they could not be meritorious: as neither would they be if they were done without charity, which cannot exist apart from obedience. For it is written (1 John 2:4-5): "He who saith that he knoweth God, and keepeth not His commandments, is a liar . . . but he that keepeth His word, in him in very deed the charity of God is perfected": and this because friends have the same likes and dislikes. . . . 

Article 5. Whether subjects are bound to obey their superiors in all things? 

Objection 1. It seems that subjects are bound to obey their superiors in all things. For the Apostle says (Colossians 3:20): "Children, obey your parents in all things," and farther on (Colossians 3:22): "Servants, obey in all things your masters according to the flesh." Therefore in like manner other subjects are bound to obey their superiors in all things.
. . .

On the contrary, It is written (Acts 5:29): "We ought to obey God rather than men." Now sometimes the things commanded by a superior are against God. Therefore superiors are not to be obeyed in all things.

Reply to Objection 1. When the Apostle says "in all things," he refers to matters within the sphere of a father's or master's authority. . . . Man is subject to God simply as regards all things, both internal and external, wherefore he is bound to obey Him in all things. On the other hand, inferiors are not subject to their superiors in all things, but only in certain things and in a particular way, in respect of which the superior stands between God and his subjects, whereas in respect of other matters the subject is immediately under God, by Whom he is taught either by the natural or by the written law. 

. . . Religious profess obedience as to the regular mode of life, in respect of which they are subject to their superiors: wherefore they are bound to obey in those matters only which may belong to the regular mode of life, and this obedience suffices for salvation. If they be willing to obey even in other matters, this will belong to the superabundance of perfection; provided, however, such things be not contrary to God or to the rule they profess, for obedience in this case would be unlawful.  Accordingly we may distinguish a threefold obedience; one, sufficient
for salvation, and consisting in obeying when one is bound to obey: secondly, perfect obedience, which obeys in all things lawful: thirdly, indiscreet obedience, which obeys even in matters unlawful.

(end quote) 

It should now be clear that Catholic Doctrine in no way endorses obeying an order from a superior when that order is sinful.

EVEN IF the Pope himself commanded a bishop to protect a pedophile priest, that Pope would be issuing a sinful order that should not be obeyed, according to Catholic Doctrine. 

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IV. Catholic Doctrine regarding excommunication. 

From The online Catholic Encyclopedia:

http://www.newadvent.org/cathen/05678a.htm 

Effects of invalid or unjust excommunication 

An excommunication is said to be null when it is invalid because of some intrinsic or essential defect, e.g. when the person inflicting it has no jurisdiction, when the motive of the excommunication is manifestly incorrect and inconsistent, or when the excommunication is
essentially defective in form. Excommunication is said to be unjust when, though valid, it is wrongfully applied to a person really innocent but believed to be guilty. Here, of course, it is not a question of excommunication latæ sententiæ and in foro interno, but only of one imposed or declared by judicial sentence. It is admitted by all that a null excommunication produces no effect whatever, and may be ignored without sin (cap. ii, de const., in VI).

(end quote) 

It should now be clear that any excommunication threatened for disobeying a sinful order would have no effect, thus rendering it not a threat. 

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To sum up:

1. Those priests who committed those crimes sinned, according to Catholic Doctrine.
2. Those bishops who covered up those crimes of those priests, even including the Pope, sinned, according to Catholic Doctrine.
3. Any order to sin, even if it came from the Pope, cannot be lawfully obeyed, according to Catholic Doctrine.
4. Even the threat of excommunication, for disobeying a sinful order, cannot lawfully be carried out, and thus cannot really be considered a threat, according to Catholic Doctrine.