Clerics were not permitted to have sex after ordination. The fact that some of them did and that two popes were supposedly born into clerical families does not mean that this behavior was licit. If you want a modern analogy, consider this: although the Church prohibits contraception, many Catholic couples use artificial birth control. However, this does not mean that the Church's law against contraception does not exist or that it should be abolished. It just means that there are many disobedient Catholics. Similarly, there were some unchaste, disobedient married clerics who continued to have conjugal relations after ordination even though this violated Church law.
What ecumenical council reached that decision?
Saying that is so does not make it so. If that was the case the Pope would not have allowed Eastern Catholics this ability.