In the Summa Theologica, part II., question 19, article 5, “Does erring reason bind,” Aquinas answers in the affirmative, even saying that this is the same as asking whether an erring conscience binds. He states: He goes on to say that to believe in Christ is good, but if our conscience says otherwise, we would be erring to believe in Him. It is the same with the Church. His words: “In like manner, to believe in Christ is good in itself, and necessary for salvation: but the will does not tend thereto, except inasmuch as it is proposed by the reason. Consequently if it be proposed by the reason as something evil, the will tends to it as to something evil…[and] absolutely speaking, every will at variance with reason, whether right or erring, is always evil.”
Therefore, to will to follow Christ or His Church, if your reason says not to, is a sin, even if your reason is in error.
The Catechism doesn’t say it is okay to WILLFULLY leave the Church. We’re talking about those who leave the Church NOT willfully, but because an erroneous conscience tells them to. The Catechism talks about THAT, in paraphraph 1970 and on:
“1970 A human being must always obey the certain judgment of his conscience. If he were deliberately to act against it, he would condemn himself. Yet it can happen that moral conscience remains in ignorance and makes erroneous judgments about acts to be performed or already committed. … If…the moral subject is not responsible for his erroneous judgment, the evil committed by the person cannot be imputed to him. It remains no less an evil, a privation, a disorder. One must therefore work to correct the errors of moral conscience.” Aquinas says it is. “[W]hen erring reason proposes something as being commanded by God, then to scorn the dictate of reason is to scorn the commandment of God…[and] conscience is a kind of dictate of the reason.”
source] Yes, their conscience is flawed, but they must obey it because it’s all they’ve got. Thomas Aquinas states that to will against conscience is sin, even if the conscience is in error. “[W]hen erring reason proposes something as being commanded by God, then to scorn the dictate of reason is to scorn the commandment of God.”
source] They aren’t okay. They are teaching error, and either they do not realize it, which is bad, or they do realize it, which is worse; but in the latter case, if they teach error without realizing it, they are not blameworthy. It is the same with one who leaves the Church: if they do not realize that they are in error, they are still in error, but they are not blameworthy, and will not go to hell for their ignorance.
I second what the poster above us stated: if we insist on the primacy of conscience, without explaining that conscience needs proper formation, we lead people astray. To follow conscience, without proper formation, is to follow error. I am sorry that I didn’t make that clear enough in my initial post. However, what I stated, was not false.