Here is where I disagree. I don't think he owes anything to the remaining sisters for what happened during the experiment. I don't think he even feels that way himself, despite disliking the slaughter. He is an evil dude and the imoutos aren't quite normal either, so it's a more or less moot debate in any case. Who knows whether Last Order decided to help him to repay or simply to be able to stay close to him.
If somebody really owes anybody anything, it's the scientists and whoever was backing them. In that sense I don't know why Mikoto is so worried: They would hardly be able to use the old subjects anymore and furthermore would make a really good target out of themselves.