Pluralism isn't actually inevitable in schools of religion (if one wanted to study in an environment of nothing but conservative Southern Baptism, one would be spoiled for choice), but it's probably the only philosophy that would work when training ministers at a place like Harvard. Critiques of religion, possibly including those Bieber has, are interesting and worth considering, and probably are considered at more doctrinally self-assured places like e.g. Notre Dame. If that's the sort of thing Bieber wanted to study, however, he should have found somewhere else to do so. It's almost a archetype of the asshole atheist, that he would want to proselytize for his atheism in the same institution in which others are training for religious ministry.
I like to describe myself as being vaguely 'militantly agnostic'[1] ("I don't know, and you don't either," as one of my favorite bumper stickers reads), and so this quote from the OP resonates with me:
But I wondered if she hadn’t swung too far in
the opposite direction, associating propositional
inquiry with religion-haters and then dismissing
it entirely.
Our type seem to nowadays have no home in discussions of not only religion, where you would expect it, but also philosophy, where naturalism is a weirdly embattled position accepted even in weak form by only half the field.
Personally, it does feel "ideologically homeless" to find that I'm largely locked out of discussing larger questions with people simply because I have only truths and no Truth.
'''Anthropologist Michael Jackson once summed up the HDS ethos. “You don’t walk up to people and tell them their beliefs are wrong,” he said. “That’s just rude.” '''
If your quoted sentence were true unqualifiedly, then science could not exist. Science is shaking-your-beliefs-as-a-way-of-life. Every single day.