You are correct, voting R or D does not in itself mean that a person is not voting their conscience. But, there are many here who are voting R simply because they believe Republicans to be better than the alternative, not because they believe in the Republicans.
If you disagree with the majority of what the party has done, as I do, and vote that party anyway, you might not be voting your conscience.
If you cast your vote for R and then think, "I hope they don't screw it up too bad, but, at least I'm not voting D.", then you might not be voting your conscience.
If you are mad at the Rs, but vote for them because you believe voting I or L will be "throwing your vote away", you might not be voting your conscience.
That, of course, is solely your opinion. Based on what, I have no idea, unless you mean that you're judging people who don't agree with you as not voting their principles.