ok i just thought of this...maybe she dies before he gets the symbiote...she gives him a speech of how proud she is of him and all that, and how he's a good person. then she dies. then he gets the symbiote and goes bad...and nothing makes him realize anything, not even m.j, but then he remembers aunt may's words and then realizes somethings wrong but doesn't know what to do, then the whole bell in the church gives him the answer he needs.
i don't know, but i thought since in spidey 2 aunt may gave him the power behind the words to realize he needs to be spider-man...why can't her words in this one help him to realize hes a hero and not a bad guy and help him to realize that what he's doing is wrong.
just a thought