Instead of punishing those that win the fortress early on by relocating them, make them move. Days of recovery are needed if you have a level 60+ base, and with 25+ bases it takes a lot of time. Those wishing to remain on the world will move however as they amass terabytes of crystal and tiberium to get to the next base.
Make them move by extending the period of the fortress revenge attacks as well as the range until the shields drop again. That way they can't be in the centre and if it is an enemy that takes over, they can only attack from the edge of the revenge area. Maybe increase the revenge attack time and range every time the fortress falls forcing them further and further out from the centre.