I experienced exactly this issue with Warhammer Online. The crazy part is that this was the Steam version of the game. (Im guessing the same programmers are involved here too, shrugs)
In any way, this problem occurs since Steam starts the launcher, and swtor then launches another exe AND closes the launcher. Steam thinks the game is terminated and status goes back to not in-game, loosing the overlay.
My guess it all comes down how the launcher handles the executed file. If the launcher would have stayed active when playing it might would have worked. In the end Bioware needs to change the manner the game is started. And i am pretty sure, that ain't going to happen anytime soon. Perhaps if they see any point in having the launcher active for downloads or something then it will work. That or if they'll change this just to please us Steam'ers.
I sure hope so.