If a game like STO can do okay for 2 years on a pay to play model with a much smaller dev company behind it, (30 employees) and much less money backing it then TOR has nothing to worry about.
Not to mention, SWTOR is almost superior in every conceivable way to STO even in its current form. STO has a significant lack of content on the federation side and feels very much like a grind even with the large decrease in XP to level. The Klingons are still only half built as a faction even after 2 years of development and are still very grindy and both factions are suffering from a lack of end game content.
I think a very understated problem with SWTOR is the lack of a trial. They say when running a store getting them in the front door is half the battle. BW are currently charging people 40-50 euro just for people to TRY to see if they like the game, which I think is a significant deterrent in getting new players.