This may sound mean, but I have somewhat of a pessimistic view of friendship. So tell me this: Do you think if Vada and Thomas J never met, Thomas J would have lived? Then the movie wouldn't have to be so sad (even if there wouldn't be any story). It could also work on some films carrying a similar senario of that part.
Also, if your head's up on some cloud, you oughta wish that the movie/chemistry between Vada and Thomas J was more passionate romance and less immature friendship... like Bridge to Terabithia.
Of course Thomas J. would likely never had died of anaphylactic shock if Vada and he weren't friends. It was a rather unique situation. Which isn't to say, as the above poster mentioned, that he might not have been in a bee-related accident later in life considering it doesn't take many stings to kill someone with an allergy to the poison, just that the likelihood of it would probably have been slim.
I don't see how it matters, though. On a smaller scale, Thomas J. may never have died if Vada hadn't accidentally dropped her ring. Or had he not been friends with her, he might have died young anyway in a completely different situation, like being struck by a car while he was riding his bike. There's no way of knowing what paths in life will lead you to fortunate or misfortune.
Also, the kids in the film are supposed to be 11-years-old. It would've been silly and unrealistic for the film to try and depict them having a "passionately romantic" relationship. They were children.
If the allergies were supposed to be what killed him, they probably should've picked a better death than being stung by a horde of bees. Not sure but don't think you'd need to be allergic to bees for that to turn fatal.
The dark writer in me would've offed TJ in a different way. The allergies would've been a red herring and maybe that tree limb would've given way and he'd drown. :P
__ Writing is my favorite hobby. Writing something that many can enjoy is my favorite dream.