Re: but ew, cooties!
I think the general consensus of the people bothered by the "spider-spunk" subplot (from what I've seen) aren't so much bothered that Peter didn't decide to use a Geiger counter before having sex with Mary-Jane but just the squick factor of his bodily fluids giving her cancer over a period of time.
I don't think Peter has ever used a Geiger counter in any continuity before having sex. He already got MJ pregnant before and never thought to use it then. And I doubt he used it when he had drunk blackout sex with Michelle either or sex with Felicia either.