Antonio witnesses four deaths when all is said and done, but two of them stand apart, because they're murders. Whether the death of Lupito, himself a murderer, at the hands of the town mob that includes Antonio's dad is justified or not doesn't change the fact that he is the victim of a violent murder. Raving in the river, he's shot down by multiple bullets, and Antonio witnesses the whole thing.
When Lupito dies in front of him, Antonio almost immediately questions, "Did God listen? Would he hear? […] And where was Lupito's soul winging to" (2.320-321). This is the first time Antonio truly starts to question God's presence, as well as the fate of one's soul. From what Antonio has been taught, the fact that Tenorio's a straight-up murderer should ensure his place in Hell. Yet later, when he witnesses the madness and pain in Tenorio's eyes as he dies, Antonio starts to wonder if someone like that should not be forgiven.
As for Narciso's death, well that lays a different kind of groundwork for our kid Antonio's spiritual grown. For one thing, Antonio not only witnesses Narciso's death, he serves as the man's final confessor. But he finds absolutely no peace in this. Instead, it causes him to rail (or at least to want to rail) against God:
I had not held Lupito while his body went cold. I had not bloodied my hands with his life's blood. I looked at the wound on the chest and saw the blood stop flowing; rage and protest filled me. I wanted to cry out into the storm that it was not fair that Narciso die for doing good, that it was not fair for a mere boy to be at the dying of a man. (14.1019-1024)
These two murders stand out as major events in Antonio's youth (that's a no-brainer), but in a way, they fracture or even shatter his childhood—pulling him irrevocably into manhood. Witnessing these murders is a big part of why Antonio grows up so stinkin' fast.