I agree - if someone offers prayers or blessings or other generic well-wishes, then I just thank them graciously, as it's meant to be kind. But if someone says, for example, "Jesus will heal your body! You just need to have faith in Jesus, and he'll get you through your surgery," I find that preachy and obnoxious. Depending on my mood, I might say, "Actually, Artemis is a far more appropriate deity for this sort of thing," or "I don't need your imaginary friend's help. I think the doctor will do just fine."

I like your strategy for reclaiming privilege from a non-privileged standpoint. That's similar to what I often do, but I like to hear examples. My own office is generally awesome. None of that stuff ever happens in my office. We all seem to be pretty liberal, and theism and religion just isn't relevant to our office discussions. It's people in completely different segments of the facility. I'm just glad I don't work directly with any of the ones who are like that.