That’s pretty much the way I see it.
Here's what I think is the next question:
A law is passed requiring John Doe to do something he thinks is wrong. What are the moral implications of his refusing to obey the law? I can see the HE would appeal to some "absolute justice", as in, "I will not kill Jews because they are Jews; it is just flat wrong to do so." Would you say that the law had been duly passed by duly elected legislators and the order was lawful so his refusal to obey it is not only unjust but a selfish preference of his whim over justice?
I read somewhere that some Nazi soldier refused to shoot some Jews and was himself summarily executed. I consider him a hero, and by that I THINK I mean something more than "I like what he did." I think the people who shot him did something wrong, by which I THINK I mean something more than "I don't like that."
For me conscience is the apprehension, sometimes mistaken, of right and wrong as they apply to a particular deed or cluster of deeds. And, with Aquinas, I think that one should (a) inform one's conscience to the best of one's ability and (b) Follow it, so that it is always wrong to go against it.
I think, for example, that Luther was wrong is his take on the Catholic Church. But I also think that, since I assume he was sincere and had given it all his best shot, he was right to follow his conscience in resisting the Church.
But it SEEMS to my dumb head that the consequence of what you think would be that Luther was "unjust" but it doesn't really matter. Is that it?