You can hop over those planets using transport ships or just flying through if they're lightly defended. Cloaker starships work too, if you clear the tachyon guardians. If you go past the bad planets, you can use a colony ship to set up a base on the good ones, and that will spread supply. You don't need supply on a planet to take control of it, just a colony ship.
You can neuter the bad planets by taking out the guard posts and warp gate, which really limits their ability to attack you. It doesn't eliminate it,but it slows it down. Be sure to leave one warp gate near a defended world alive, so the Ai will attack that one with waves.