No one is arguing about the Primacy of Conscience or against Thomas Aquinas. It is quite clear that anyone who believes his conscience is telling him to do good and acts against it intends to do evil. No one is arguing about that either.
The question is to what extent does one's conscience have the authority to override the Magisterium? You obviously believe that each one of us is the supreme arbiter of what is right and wrong and not the Church which receives its authority from Christ. This is much like saying as did Adam that one is greater than God.
If one sincerely believes that the Catholic Church's teaching is false then it is very difficult to understand how one could honestly remain a member of it. To say, "I believe in the Holy Catholic Church would be a complete lie."