If I have a thought or feeling that says I should do something that violates my conscience, I am very wary of doing so – and I have to take a long, serious look at why it might be okay to do it. There are multiple reasons why I still might do it, but I would have to study it out in my mind, find a reason I could accept and then re-examine it in my heart before I would do it – and that is true no matter the source. I believe doing something that violates my conscience without such soul searching is relinquishing my agency in a very real way. If I make a mistake in that arena, I would rather err on the side of my conscience than on the side of violating it.
If, however, I consider something that I simply don’t want to do, the consideration becomes much easier – based on whether it would violate my conscience to do so and what the impact of my action would be on others.
In a nutshell, I try to base my actions in these situations on how I believe those actions would “hang” under the two great commandments – and it takes a truly extraordinary situation and what I consider to be indisputable, extraordinary revelation to make me go against those two commandments and/or my conscience (and how I view the two great commandments might be a good definition of my conscience).