I've worked in Boston, NYC and DC so I get the professional culture in these cities. Obviously, this kid does not.
To start, he shouldn't have debated/argued with you about what kind of clothes he would need to wear to be successful in your industry. As a newcomer, he needs to be learning (even in the job interview) from those with experience in the industry. I have also found that it's a red flag if any candidate is argumentative in an interview especially on one of the first questions/comments. He should have enough self awareness to realize what you were saying...if you're going to be successful here you need to present yourself in a different way.
And then the overemphasis on the mission...that's also a red flag. As you point out, there are some things that a candidate can demonstrate from his/her mission experience. But it's not really directly applicable in most jobs and usually shouldn't be emphasized (I understand there may be exceptions to this). When I first started working I used my mission as an interesting footnote on my resume and sometimes it was a novelty to discuss in an interview, but mostly people didn't bring it up because they didn't want to talk about religion in a job interview. I would have taken that emphasis as a bad sign too.
So I think you did the right thing, and I did not get a sense that there was any religious bigotry on your part. I'm not sure where that idea came from. I'm LDS and I wouldn't have hired this kid either for the same reasons you didn't.
And don't worry too much what some CBers post. The anonymity here is part of what makes this fun, but it also allows people to say negative things they'd never say in person.