Moving the Ba'ku to another planet without their knowledge...
It could have worked on the primitive folks of "Homeward". But the Ba'ku are seasoned starfarers, and would immediately notice what had happened. The Federation does not realize this, hence the holoship, but Rua'fo would have known this all along.
Who hadn't been in space in at least three centuries. Keep on reaching...
EDIT: And let's be clear on one thing, it isn't Ru'afo who breaks the agreement. It's Starfleet by being unable to control one of their starship captains.