I think a lot of people are missing a key point here. This isn't about stopping a candidate you disagree with, or even about stopping a candidate that you think would be bad for the US. It's about making Y Combinator and the software industry as effective and good-for-the-world as possible.
Even if throwing Thiel out would actually help Trump's candidacy, they should do it.
There's an interesting debate about whether you think Trump's policies are a good idea, and how much you care about him being elected, but that's a sideshow. Thiel represents Y Combinator, like it or not. How he's perceived affects how Y Combinator is perceived, and how the industry (SV especially) are perceived by the rest of the world. Currently, he's actively and very publicly giving millions of dollars to a candidate espousing violence, sexism, racism and sexual assault.
By supporting Thiel, Y Combinator is supporting somebody espousing violence, sexism, racism and sexual assault. It doesn't matter if they're a presidential candidate or not, or what it does to the election results. Encouraging and supporting these _moral_ positions is horrific, bad for everybody, and just practically bad for business. When your public face becomes the face of hate speech, you have a practical business problem, and you need to solve it.
You would fire a public face of your company if they publicly wrote a post about how they liked to sexually assault people. You would fire a public face of your company if they publicly donated millions of dollars to an organisation encouraging sexual assault. Why is it different if the organisation they're supporting is running for president?
It's not about Trump's policies, and it's not about whether or not it plays into Trump's hands: if a major face of your business is actively visibly supporting abuse, discrimination and violence and you do nothing, then your business is supporting abuse, discrimination and violence. You're going to give you and your industry a bad name and discourage minorities of all kinds from ever working with you, along with anybody else who finds your morals repugnant.
Supporting Thiel while he actively defend and encourages racism, sexism and violence in the name of "free speech" doesn't make the world better; it makes it far far worse.