It's common for Roman Catholics who disagree with Church doctrines to invoke Church doctrine on conscience as proof that their disagreements with Church doctrines is consistent with Church doctrine. Quite often they will point out that St. Thomas himself taught that one must follow one's conscience, even if that contradicts what the Church teaches.
It's certainly true that St. Thomas taught that an erring conscience binds. He could hardly have taught otherwise, since he regarded conscience as the act of applying knowledge of moral principles to deciding what should be done. To act against your conscience is to choose to do something you judge to be evil, and it is always evil to will evil.
That said, St. Thomas is not a safe authority for dissenters to invoke. The same article of the Summa Theologiae in which he argues that conscience always binds includes the following objection:
...according to Augustine, the command of a lower authority does not bind if it be contrary to the command of a higher authority: for instance, if a provincial governor command something that is forbidden by the emperor.
St. Thomas replies:
The saying of Augustine holds good when it is known that the inferior authority prescribes something contrary to the command of the higher authority.
In other words, St. Augustine is right: the decision of an erring reason does not bind when it is known that the erring reason prescribes something contrary to God's commandments.
This raises the question, how can we know when our reason prescribes something contrary to God's commandments? We need to be able to recognize a contradiction when we see one, and we need to know God's commandments. How do we know God's commandments? He has revealed them, and founded the Church to teach them to the nations.
If, then, I know that the Church teaches that God commands something, and I know that my own judgment is that I should do something contrary to what the Church teaches God commands, then I know that at least one of these two things must be true:
My reason is in error, and I should not follow it.
I do not believe that the Church teaches what God commands.
Now, if I don't happen to believe that the Church teaches what God commands, then I don't believe it. But I can't at the same time claim to be acting as a faithful Christian.