The reason I'm making a case for Ben is that he gets blamed for a lot more than he actually does. Sayid wasn't totally justified when he pulled the trigger. How could he weigh the amount of good vs the amount of bad that Ben has done, especially since he himself is no moral person - woman torture, assasination and multiple betrayal ?
I don't believe Sayid killed young Ben in an attempt to seek revenge for the terrible things that Ben had done (both to others and to him). I believe Sayid was attempting to avoid those terrible things from happening by killing the perpetrator before he had the chance to commit those terrible acts. Sayid hasn't been briefed by Daniel as to the "What ever happened happened" theory so he (as I imagine most of us would do) thought he could change history. Sayid shot Ben to save the Dharma Initiative from the purge, to save the Losties from their persecution at Ben's hands on the Island, to save all the people who were assassinated by the Sayid-Linus team, and to save himself from Ben's manipulative clutches.