Modding community thinks so too. Like with many other mods, MechJeb can be restricted to operate only when appropriate parts are included on your vessel, and those parts are unlockable in the tech tree.

There's a mod called Community Tech Tree, which exists solely as a way to incorporate other mods into a somewhat coherent, extended tech tree.

You unlock kOS with the tech tree. And you need to write the code yourself/ or copy from github. So I think that's reasonable.