On the scale of techies trying to ruin people's lives, I'd put the level of these donations pretty low down the list of concerns myself, even if I don't love them (Peter Thiel's right-wing donations worry me more, for example, because they are much, much larger).
I don't mind money going towards Libertarian asshattery because frankly, I'm happy to see it crash and burn as publicly and spectacularly as possible.
Or not. In which case I'm prepared to change my views. But I'm not prepared to change my view about the 14th Amendment and the wisdom and decency of assuring basic legal equality for everyone. To my mind, that is an entirely settled issue. I'd no more go back on that than I'd tolerate a return to slavery (which, let's not forget, is the horrible error that necessitated the 14th in the first place).
You are happy to implicated in some bullshit libertarian experiment to see if it crashes and burns, harming many people, but are offended about being implicated in some bullshit Christian experiment to see if it crashes and burns, harming many people? To me, the collateral damage of Christian fuckery and libertarian fuckery are roughly comparable.
But in any case, Thiel gives money not only to candidates of the Libertarian Party, but also (in fact, mainly) to the regular, anti-gay GOP. It could be that he hates gays. It could be that he doesn't, but just considers funding anti-gay propaganda to be acceptable collateral damage in a quest to promote the Republican Party's other positions. Either way, he's a much bigger problem in my mind than some small fry giving 4-figure amounts to them, because he's giving 6-figure amounts to the bigots, which they can use to promote bigotry.