As I've said in the past, I don't exactly hate KOTOR: it's just the stupid Darth names and red lightsabers I particularily dislike. Regarding TOR, whatever references there were to that game I completely missed.

As for overwriting TOTJ, I guess the bit with the forcesabers does conflict with the protosabers used by the Jedi during the Great Hyperspace War, but I can think up a few hypotheses to make it work. Even if I couldn't, though, it's only the basic storyline and characters of DOTJ that I concretely accept as a part of my SW Universe; the surface details can be easily discarded.