Please forgive the sarcasm, but:
Yes, and the practice in the 1st century was to pray in catacombs and outside cities, so let's get rid of churches. Clerical celibacy was endorsed through most of the game's timeline, although, from what I remember, certain low-ranking members of Holy Orders didn't have to take the vows. Still doesn't explain why married men with children can become Catholic bishops (orthodox bishops would be an even-harder to explain case as they generally come from monasteries, mostly only lower-ranking priests marry). At the very least limit it to childless couples.
Please forgive the sarcasm, but: Vassals weren't supposed to rebel against their liege so maybe they shouldn't in CK2? In the Catholic church men who became priests while married could retain their marriage but could not engage in intercourse. Different rules were decreed at different times by the Orthodox and Catholic churches. Even as late as the 1100's many country priests and even Bishops were married and had children. In the 14-1500's you still have prominent married clergy. Martin Luther, Thomas Cranmer who was named Archbishop of Canterbury while married. Rodrigo Borgia was voted Pope even though he had multiple acknowledged bastard children. Even now in the Orthodox Church a married man who becomes a priest can keep his marriage, but cannot remarry if his wife dies, and celibacy is only required of bishops. So just because the technical rules stated that priests couldn't be married, bishops couldn't have children etc. it was actually fairly common for MOST of the time period. Your argument is kind of like saying that because the catholic rules forbid Antipopes and there weren't a ton of them then they shouldn't be in the game.