Like Entropy suggested, what about adding a lower cost prereq ability for the early game and make the current ability more time consuming to research. How about have the early tech reduce the soldiering ability of the planet and/or reduce the population by 50%. It that isn't useful enough in the early game it could reduce or stop population growth and/or production for a set amount of turns.
I don't quite understand how this SA made it to the game, if you take into account the arguments used against planetary bombardment... even forgetting that little detail, how you gain control over a planet with no presence there, even after obliterating the opponent's presence, is strange.
This idea, conceptually it's a better implementation of the tech, even though those 50% are still genocide. Reducing planetary output at all levels is good for an early game ability, but I'd say the opponent should have to research the early tech to get rid of the effect, instead of working for a # of turns. Forces the opponent to divert resources to research an area he might otherwise not touch at all.
To be honest, this shouldn't even be a SA, but a tech available to all civs. Sounds better than some if not all invasion tactics...