Yes, it most certainly does. I used to be a submarine officer in the Navy, but I was discharged 2 years ago as a conscientious objector [1]. I left because I felt I had a moral responsibility to do so.
If your conscience says "don't kill someone," then you shouldn't kill them. You can't absolve yourself of responsibility just because the president ordered the killing.
[1] http://www.nytimes.com/2011/02/23/nyregion/23objector.html?p...