Also, is there a way to launch the game directly by running the .exe file instead of the launcher?
SWTOR does not provide in-client login that I've seen, so unless you're going to develop your own launcher to get the keys to pass to the client I wouldn't hold your breath.

As far as running as Administrator, if you're not using ISBoxer (multiple PCs?) then I don't think it will be so simple. For those playing SWTOR on one PC with ISBoxer, Inner Space should already be running as Administrator, and then each SWTOR instance will be launched as Administrator so you shouldn't get the popups.