A human being must always obey the certain judgment of his conscience. (Catechism of the Catholic Church, #1800)
The Catholic Church puts a lot of emphasis on our conscience. It allows us and even invites us to wonder, question, and disagree. So what exactly are we supposed to do when our conscience disagrees with Church teachings?
The answer again comes from the Catechism:
A well-formed conscience will never contradict the objective moral law, as taught by Christ and his Church. (Catechism, #1783-5, 1792, 2039)
This echoed what a priest said at a retreat I attended two weekends ago. Someone asked the priest what we’re supposed to do if we disagree with something the Church teaches. He said, “Assume the Church is right, first of all. Then ask yourself where in your line of thinking you start to diverge from what the Church teaches. Take that one point, and learn more about it through diligent reading and talking to your spiritual director.”
Does this mean that in the process of forming our conscience and learning about the moral law, Christ and his Church, our disagreement will cease? Yes! We make a pretty bold statement when we say that Church teachings are infallible, that the Church is the fullness of the Truth, and that if we gain knowledge of that Truth we will end up in line with Church teachings, but that’s what we believe!
So if we have questions about and disagreements with what the Catholic Church teaches, we must ask, study, and pray! Obviously, learning our faith and forming our moral conscience is a daily and lifelong process. Thankfully we have the lives of the saints to give us hope and encouragement!
FWI: This website offers a concise and valuable explanation of moral conscience.