I'm out of my depth here, but it seems to me one idea could be to help bacteria evolve rather than aim to kill them all. What I mean by this is that perhaps using bacteria against themselves could be an interesting approach. Much like over decades people bred dogs to encourage certain traits perhaps we can coax bacteria into developing traits that help us rather than help them when they come into our bodies. Maybe your run a fever for five or ten days and feel crummy but rather than have bacteria trying to destroy you they are, effectively, fighting and destroying themselves.

In other words, Aikido not Karate. Use their own energy against them.

Just a thought. Probably nonsense. Not a biologist.