They are useless right now, but I don't think when a new codex comes around they'd just move them to a merc' dex or what have you. I mean thats just more absurd that you'd have to take units that used to be in your codex as allies.
And here's why it's a stupid idea to remove them entirely.
Guy1: Ok, we are making the Tau 6th ed Codex. One problem is Kroot. They just don't really have a good place.
Guy2: Well, we're making the codex. The possibilities are endless on how we can make them better. We can change their equipment, give them special abilities, give them new options and units. The precedent for this has already been set and there are tons of ideas we've already experimented with.
Guy1: So it's agreed then.
Guy 1&2: Remove Kroot entirely from the codex! (They said in a strange unison that made you question wether or not they rehersed the entire event.)
"Snooki gives birth to Heavy Gun Drone squad, someone says they are over powered, then the world ends."