Do I have to leave the Church, if my God-given conscience is telling me that some Church doctrines is immoral?

Sadly, people place more meaning in their religion then their faith. Nowhere in the bible, old or new, does it state that you should follow this or that religion. Only that you should believe in God and Jesus and that He died for your sins, etc. That is what makes you a Christian and I believe that is all that matters in the long run. Don't let any religion dictate what you should believe, if it doesn't feel right to you.