I'm pretty familiar with the multiple UTEOTW interps, it is stronger live "we broke the bread, we drank the wine". I can see Vertigo both ways personally, either as two separate levels or as mixed imagery. I don't think there were any girls who nailed Jesus to the cross, nor can I see how he would be swinging around her neck unless it was on a small necklace. A lot of lines wouldn't make much sense if you tried to take the song back to the crucifixion, ie a band playing music while bullets fly overhead... I can't think of any imagery that would correspond to this.
For a Christian interpretation I would see it more as Christ being the single thing which makes the uncertainty, superficiality, and confusion of existence worthwhile... the one thing that is pure enough to really feel above everything else, which is a part of fallen existence. It could either be in reference to the specific time we live in (Electrical Storm, etc) or just material existence in general. I suppose the uncertainty of the times take is enhanced by the changed line in the remixes.
I was actually thinking of writing up some interesting "fake" interpretations of the song to see how far I could take things while still keeping true to the words. The song really leaves a lot of room for interpretation, and it would be fun.
I should be putting up some transcriptions of ABOY and COBL soon... audience recordings from TOTP so I doubt they'll be perfect, but they should at least be more accurate than Love and Peace and Miracle Drug. Since you were there I'm guessing you'll be interested enough to take a crack at them.