Conscience should be the ultimate guide when taking a decision. Otherwise, there would be no freedom of religion if a book or a dogma can decide for the person.
In Christianity, there are two ways of explaining what conscience is: God speaking in the person's heart and a practical judgement on decisions made or still have to be taken.
It is not true that following one's conscience will lead to anarchy. If one really follows one's conscience, the person consults with the natural law one feels: that you should do to others what you wish others do to you, that you should respect your parents and legitimate authority, safeguard life, the family, truth and respect private property. One decides logically on the facts. One consults his/her faith and prudently seeks enlightenment and advice from people deemed to be honest. Ultimately, it is the person who, before God (if one believes in Him), decides and s/he does so by listening to his/her conscience.
Do not be afraid. Jesus delegated his authority to the Church and she updates his teachings according to the times. The Church is made of mainly men (and some women!) who listen to their conscience to decide whether to accept a new way of explaining Jesus' words.
Following one's conscience will make a person more responsible. One cannot abdicate responsibility ever: even when voting.
Following one's conscience can mean that a gay person does not feel guilty externalising and actuating his/her identity. It can result in curtailing one's pleasures and sacrificing them for those s/he loves. It can mean that one decides to preserve our natural environment for future generations and postpone short-term gain. One can come to the conclusion that other creatures have a right to live on our planet and that we ultimately need them for our survival.
See how healthy it is to educate a person to follow one's conscience!
Joe Portelli
Nadur