That said, the objections I'm reading here are centered around supporting a government that actively tortures political activists and captured enemies. I think the phrase "if you [disagree] with their political views" trivializes that position.
Unless you're designing some kind of torture software, I think you're massive reaching to make one apply to the other.
Nothing about doing better e.g. tax software, road planning, or similar is going to help the US Government torture detainees.
Realistically there are millions of US Government connected jobs, it is just unrealistic for everyone to boycott them because another part of a massive government did something ethically and morally wrong.
I suppose you could counter that the abhorrent practice of intentionally wasting resources to ensure that subsequent budgets don't shrink will tend to prevent the torturers from getting the additional funds you free up with your advanced tax or road planning software, but there remains a good chance you'd free up resources for something within the department that would cause someone to be worse off than they were before. The only winning move is not to play. (OK, that was an opinion on the gov't)
Of course, that implies that U.S. citizenship is already tainted---if you aren't actively protesting, working for the government in an unrelated area isn't any worse.