Sure, can relate, although I'll be honest that OMD's mere existence bothers me more then the mechanics, if that makes any sense; crap stories happen all the time, just a question of whether it affects the rest of the series or not. (Still think that if it had to happen like that, it needed to be MJ herself, not Aunt May, dead/dying for it to "work").
I frankly don't know the exacts of the more atheist-centric Spidey stories (or miniseries?), although at least one apparently ended with him reconsidering his position and talking to a minister character who'd appeared before. Only heard about because of a fan online who was complaining about them as they came out (although, since the guy in question is quite the entitled jerk, I didn't exactly put a whole lot of stock in what was being said about it).
(Kinda have to admit that I'd be curious to see religion explored more; when pagan gods are a fact of life and heaven, hell, and other supernatural places can be visited under the right circumstances, how does that affect real-life religions that exist in that world?)