Yes, yes they will: http://www.patheos.com/blogs/friendlyatheist/2017/06/23/maaj...
I don't think Maajid Nawaz is going to win because he'll have to prove real damages from the SPLC (horribly erroneously, in my opinion) labeling him an "anti-Muslim extremist". Being put on a blacklist by YC might result in damages that are easier to prove, though.
I think this is less likely to be legally complicated than you think. Consider: YC has been doing this for years already.
EDIT: When it comes to conferences and professional organizations, I think those things are more like a bakery than like YC. A programming conference is in the business of fostering discussion of and dissemination of information about programming. A code of conduct is fine for such an organization, but a politicized code of conduct has no place in such an organization. There's something clearly wrong with politicized code of conduct in a non-political organization that makes a subset of its members uneasy. There is no place for intolerance in a liberal humanist multicultural society, and people who want to use the bureaucracy of non-political organizations to alienate their political opponents are intolerant people who have given up on convincing people. Such people want to bully people into doing what they want. What they are doing is only the softest form of intolerance.