Conspiracy theory time:
MC ISN'T the same person as the little boy we see here. Why?
For one, the age gap. She seems to be one or two years younger than him in the flashback at most, yet in the events of the story, he's in college and she's 14. Sure, it might be that he's 12 and she's 8, but the way they speak is more indicative of children that haven't reached a level found around the preteen range, and more likely that they're both very, very young.
Secondly, there's the fact that MC's mother recommended the job to him. I doubt they reconciled considering burning someone's face off after years of domestic abuse isn't something easily forgotten, and recommending a job to your amnesic son where it would take him back to the place where he killed someone would probably be a bad idea. Additionally, I find it hard to believe either them stayed in contact with one another after he was sent to the orphanage and especially after the government got involved. Granted, there's the possibility that his new "mom" is a foster parent, but he doesn't specify that which he would be able to at that point in his development, as well as the former issue that he thinks fondly of his mother, meaning if she is a foster parent, I doubt she would send her child back to the place where he committed a homicide.
Thirdly, the closest MC shows to having any of the behaviors or tendencies of the kid is that he chops up the bodies himself, though I always assumed this was a guilt thing instead of him slowly descending back into a carnal desire. He's very empathetic and shows no signs of sadism or depression, nor does he indicate he has antegrade amnesia of any kind that would completely change his personality.
If I were to guess, MC is not related to the events at all and merely resembles the person she thinks of as her "Onii-chan," as we know she not in the most sound of minds. Keep in mind how this information is relied to us: it is by an unreliable narrator where SHE frames the story. It's not something MC realizes on his own.
Most likely, he strongly resembles the person she remembers-but never got the name of-and so assumes it's him whereas the "real" Onii-chan is probably in a Juvenile Detention Center, or has been tried as an adult and is long gone.
TL;DR MC isn't the little boy in this story. He's some unrelated that was kidnapped and roped into committing these crimes despite being unrelated to anything that has ever happened in the Orphanage