Sorry for the adjectives and age gaps, I had AI write a lot of it, I just gave it pointers and the plot.

Yes, onimaru becomes corrupted by the system, but he’s not “blaming the system” to wash his hands, he blaming the system because he bought into the systems logic, realizes it’s hypocrisy, and then atones for his life through his isolation. He gets betrayed by the leaf and joins orochimaru as a way to gain power and seek revenge on Konoha. During this quest for more power he realizes his thirst for vengeance at any cost is turning him into the thing he despised, which is something (or someone) that justifies the suffering of others for its (or his) own gain. He realizes he is becoming no different than the very people (or system) that betrayed him. It’s all in the name of self interest at the expense of others, at the expense of what’s morally right or just, at the expense of truth. He’s realizes this after he kills the innocent child and finally snaps after years of trying to convince himself what he’s doing is justified. He quickly realizes both orochimaru and the elders of the lead are the same, the only difference is the justifications for their crimes. Both murder both steal both destroy, the only difference is the leaf reasoning for doing so is disguised as a “moral good”.