First of all, if your 'good conscience' manages to suggest Clinton (a flawed but relatively competent candidate) and Trump (a racist orangutan with a string of failed businesses and shady deals) are somehow equivalent then your "good conscience" is a failure. Trump is a racist nut-bag, Clinton was not. Not doing everything you can to stop Trump means that you consider things like the forced separation of children from parents to be less significant than it really is.
Secondly, the U.S. is (for better or worse) a 2 party system. If one of the candidates is REALLY bad (like, for example, a racist orangutan who tries to equate Mexicans with "rapists" and who eventually brings about a situation where children are forcefully separated from their parents) it makes sense to want them stopped. A vote for a 3rd party says "Errr.... racism is no big deal".