I'll agree that it is most likely that Rupert was just over-excited, or got confused. The noise was probably driving him mad, and he had no clue why your brother was making it. For all Rupert knew, it could have been that your little brother was scared or hurt, or trying to hurt him, or playing or anything... too much stimulus that he just didn't know how to respond to. Doesn't sound like an aggressive reaction, so no need to even consider putting him down. Hopefully, in a worst-case scenario, your mom would at least give you time to try to rehome him some place without small children.

Maybe you could also work with Rupert and various noises? Nothing to torment or hurt his ears a lot, just make noises of all sorts around him, and soothe him if he starts to freak, reward him when he handles them well?