It doesn't even really bother me that she's dead, it bothers me that the death was kind of meaningless and simply a way to write Irene out of the movie. They could have done in a way to make it that much more believable and have more impact.

That being said, it's pretty easy to imagine Moriarty having secreted her away - there were a lot of drugs even back then that would make someone appear as if they were dead. And having her as something to drag out in front of Holmes at a later date makes sense to me.

(I really wish I'd liked Irene more. Guy Ritchie really let me down in that regard.)