First, if you want to vote for Jill Stein, feel free. One thing I'm adamant about is that a vote is a vote. I really dislike the Berniecrat criteria of pretending Reddit upvotes, phone-calls made, Facebook likes, "likeability" polls, etc., are a suitable replacement for voting in a democracy. If you can vote but you don't vote, politicians ignore you. You can argue "my vote doesn't count", but there's a purpose to voting beyond who literally wins the election - it's a flag of visibility.
Anyway: Here is why Jill Stein drives me nuts with the anti-vaccine thing. Most political debates and stances are based off of a fundamental disagreement about priorities or values. Obviously, things get obfuscated by the media and not everyone is working with 100% data, but primarily we make our political choices based on value judgements. I am going to side with a politician who supports gay rights not because I've sat down and poured through the scientific literature saying it's okay, but because it's a moral position I hold strongly. Likewise, if someone disagreed with Hillary because of her foreign or domestic policies, I would support their right to do so - I might argue with them over the consistency of their beliefs, specific accuracy in their narrative, and try to challenge them, but I'm not going to call someone stupid or dismiss their position because I accept people can start from an axiom that is totally far and away from mine.
The problem is, vaccines aren't like that though. The science is unequivocal - the risk/benefit ratio is astounding and they are one of the most important preventative health benefits ever discovered in the history of mankind. Stein's inability (especially as a physician!) to accept the data that they are safe, effective, and do not cause autism says nothing about her values, but is a direct reflection on her actual competence to assess evidence and come to a reasonable conclusion. To be blunt, she is not intelligent enough to be commander in chief and she is an example of my greatest fear - progressivism simply becoming a religion divorced from a science-based approach to policy.
I apologize if you feel like you're getting dog-piled and I don't want to come off as mean - I'm just wanting to try and elucidate why someone being anti-vaccine is not "just another issue" on the table that we happen to disagree about. It shows a fundamental degree of incompetence, even though in the political landscape it's not really considered a controversial topic.