One of the forefront concerns I have whenever anyone starts appealing to the primacy or even instrumental role of consciousness with regards to moral questions is this: I think people are prone to bullshit wildly whenever they can get away with it, and when a fundamental justification in their decision-making process is entirely mental, the bullshit accumulates quickly. This is one reason why it's a bad idea to argue about someone's motivations - because 'motivations' are usually known only to a single person, and said person may well be willing to lie like crazy if they know no one can really check them for sincerity.
When the Pope was (at this point, quite possibly wrong) quoted as saying that 'if everyone followed their consciences, the world would be a better place', a lot of the worry seemed to center around the fact that this gave people license to support everything from gay marriage to partial birth abortion, so long as their consciences told them it was the right thing to do. That wasn't really my prime worry. Instead it was the expectation of the inevitable nonsense that would immediately follow, where people (particularly Catholics) would suddenly discover that their consciences told them to do everything they always wanted to do, and still be able to sell themselves as good Catholics and moral people because 'I'm just doing what my conscience tells me!'