Plot, Kishi had to get rid of powerful clans like Senju's and Uchiha's from Konoha, otherwise the story wouldn't progress much, for example Oro would never attack konoha in part 1, even Pain in part 2 could be defeated, considering at that time many Uchiha's could already awaken MS. We've already seen what main 5 Uchiha's were capable of, could you imagine a whole clan of that? Well, maybe not a whole clan, but if you let them be, sooner or later there would be born more prodigies like Itachi or Sasuke, Kishi had to get rid of them asap.