Disney can't really the license agreement for Bioware/EA to use the Star Wars universe was well before the deal so Disney has to honor it till the license agreement ends.
Well without knowing the details of the SW:TOR License I can't say for certain but during development and since there has been alot of talk about work done with the team at Lucasarts and I know that most SW licensing has caveats that lucasarts/film get approval on storyline so pretty indirectly Disney will have input. On the other hand Disney has been pretty clear that lucasarts is a fringe benefit to lucasfilm and really to the star wars franchise. They want to make star wars movies TV shows and lots of merchandising not meddle with a game they have neither investment in nor profits from.
Now if Bioware goes off the rails or EA starts trying to muscle in and screw with SW canon in a way they don;t like you better believe Disney will step in but that honestly would be a good thing. For whatever faults Disney may have you can not deny that they carefully curate their IPs to ensure their continued success in their respective areas.
Honestly given recent history
at Disney my biggest concern is that the next star wars movies are going to make me weep like a child.