Origin should pick up on the SWTOR install (after you install it) even if you didn't get it through Origin. It does that for a number of other recent-enough EA titles, but not 100% sure on this case.
Either way, it will never do its patching through Origin, so all you're getting is being able to launch from it and the in-game overlay. Worst case, move the install later.
"Point being, they can't make everyone happy, so I hope they pick me." -Ingmar "OH MY GOD WE'RE SURROUNDED SEND FOR BACKUP DIG IN DEFENSIVE POSITIONS MAN YOUR NECKBEARDS" -tgr