I'm with you here. I'm not Christian either, and I don't care what others beleive in, have at it. I don't mind if someone wants to say a prayer for me in the privacy of their own private space. In fact, I think it's nice they're thinking of me. However, right there, in front of you? Yeah no.
I'm autistic (diagnosed at 48) and very uncomfortable with public displays of affection, or emotion directed toward me, so yeah, again, no.
Had it been me, and I do understand that I'm a different sort that now speeaks my mind freely without apologies, I'd have thank him and just told him that I was uncomfortable with the public nature of what, to me, is a very personal decision and relationship with whatever god he prays to.