See, I can do the "she pulled the trigger out of fear he'd eat her brains" bit, but the only reason she was pointing it at her own head (or even able to) was because he made her. I think it was "we want Sylar to kill Eden but can't have him get her powers, so we'll do this."

So, err...it was fail on Sylar's part for robbing himself of a good power, or fail on the writers' part for for an illogical setup given Sylar's wants and abilities.