OP's "what caused the faction imbalance" idea is well thought out, but it's not much more than a hypothesis. It'd take some serious polling to back it up. Like most people, I think it's much more simple than that since we see this "Bad guy faction" overpopulation with most MMOs -- even those without much expressed in their pre-launch trailers.
It's a decent idea the OP has, but with the current Ilum valor buff, it freezes most peoples' clients for a moment when it has to update the buff from a point changing hands. It can screw people over depending on when it happens.
Adding another buff that requires constant updates -- especially based on the population of hundreds of players, and not just "who controls which of 5 points" -- would only add to this issue. Hopefully it's an issue they can fix.
Then there's shard-hopping. I've seen large groups of Republic exploiting the new Ilum shards to get away from the main chunk of Empire players, so THEY'D be the ones outnumbering their enemy. OP's suggestion could either fix this (the 'outnumbered' empire in shard-2 will be stronger and able to defend against the republic), or it could have people switching shards to exploit the system (a few players switching to a shard where they're outnumbered to be super-buffed).
They'd have a lot of issues to fix before something like this can be implemented, and probably just as many issues to fix after it has been implemented.