Freud was not the only scholar to have a view on what conscience was, with St. Thomas Aquinas, a 13th Century American Scholar also trying to define what it was. Aquinas portrayed that conscience was the power of reason, between doing right and wrong. Not believing that Conscience was an inner knowledge' given to us, but rather the faculty to distinguish between good and evil, once it had been educated, and the "reason making right decisions", with it our obligation to society "..to educate your conscience so that it makes right decisions."
Joseph Butler, an Anglican Priest, defined conscience as the intuitive voice of God, which should always be followed as it is a "constitutional monarch", representing the element of Christian teachings and tradition upon our minds.
As to whether Conscience is the best guide to making moral decisions in sexual ethics is therefore entirely dependent on which view you decide to look at. If you take Aquinas' view that it is a faculty for reasoning of which we have a right to educate it, then going against your conscience would be going against God's teachings, which is wrong. However, he also says that ignorance is no excuse, saying that if a person has not educated their conscience enough to make right decisions, then they are also wrong.
Aquinas' view is very contrasting to that of Butler, who also believes that it is religion based, but instead of our own faculty to make our...