Hm... conceptually, I wouldn't mind Spidey sharing a universe with other superheroes, but I think that that should be seeded from the start. I guess one could say ASM precedes Thor, and thus could fit into the MCU without too much trouble, but that begs the question of where Spidey was during the Chitauri attack. (In bed, with a feverish case of Spider-flu?)
Who's to say he wasn't out there fighting the Chitauri? Or saving civilians?