Eh, no no, there's indeed a reason. That reason being plot progression.
But yeah, kinda weird how he didn't kill them. My guess would be the fact that he's trying to keep the changes as low as possible so he could take advantage on his knowledge of the future.
Still, if the mastermind dies, there should be no plot to be aware of, unless.... The MC doesn't think those two are the only mastermind, that's why he's being wary(?)