This is what makes me confused. While I do understand the problem described in topic; I have no problems at all with that ability (or more exact, its counterpart on the Jedi Knight - Master Strike). It was the first ability I came to think of when reading the OP, and as far as I have experienced it works, and if I fire off another spell after the global cooldown is done, but before the 3 second channel-time is finished, Master Strike gets interrupted; the animation stops, the channelled damage stops and the animation of the new spell starts. Just as one would expect it to work. I'm pretty sure most of my characters animations stops when I fire off a new spell, as long as the global cooldown is done. I will of course look deeper into it, but I can't really relate to magnitude of the problem that some people in this thread seem to experience.
Why does it seem to work one way for some people, and another way for others? It's almost as if the right code is there, but it doesn't work for everyone. Makes me believe that this is indeed a bug, and not the way the game is supposed to work.