This recent exchange with DHH may give you some insights: https://twitter.com/paulg/status/787561745686618113
If YC is saying Thiel can't be managed on that basis, he is a partner. And if he is a partner, YC can choose not to partner with him.
I could see both Goldman Sachs and YC operating under this mission statement.
As much as PG wants him to be, Thiel isn't an employee. He's a partner in a partnership, and partnerships have been dissolved for worse reasons than "offending partner is an opportunistic bigot".
This is a thing they have discussed before. If I were pg, I'd be bored with it by now.