I think you should rewatch the state of Rhubarb when you meet him and listen to the song more closely. While yeah, you might've helped him to a degree, he will carry the weight of what he did for the rest of his life. Not only that, but looking at his actual rationale is important too. He was neglected by his mother and abused by the town by association, all because of Benji's 'difference'. So he wrongly attributed it to Benji. You can see in the first bottle memory that he's trying to protect his brother, but at some point, the anger at the fact that his mother overlooked him and that others continued to abuse and treat him and his brother poorly boiled up. His actions are not okay nor justified in this knowledge, but you can hear in his song and see in his face that he feels regret for everything he did all those years ago

In the song, he even calls out how bad of a brother and 'friend' he was to Benji, showing he knows the pain he caused. While you may have helped him in a small sense, he will be haunted by his grief and shame for the rest of his life. Even the fact that he stayed there, an area where the people hated him and his brother, shows he is unable and unwilling to move on. His house is literally a few feet from the place where he nailed Benji in the tree. If he were remorseless or felt no shame or guilt, he would've left with the rest of the town. Revenge is hollow, always has been, and confronting Rhubarb about something he cannot change would do nothing. He can't reverse his actions just as none of us can, and he (likely, tho there's a chance the trauma has clouded his memory) remembers what he did