I linked a while back to George Lucas's quotes on Star Wars canon. Let me try to make things more clear here.
I think the problem, ultimately, is that Trek has never had a system for integrating those two sets of materials together. Star Wars, B5 and other franchises have done so, but Trek likely can't. They've made the choice to acknowledge one set over the other, and in doing so have cemented that separation into the mindset of many fans.
George Lucas said:I don't read that stuff. I haven't read any of the novels. I don't know anything about that world. That's a different world than my world. But I do try to keep it consistent. The way I do it now is they have a Star Wars Encyclopedia. So if I come up with a name or something else, I look it up and see if it has already been used. When I said [other people] could make their own Star Wars stories, we decided that, like Star Trek, we would have two universes: My universe and then this other one. They try to make their universe as consistent with mine as possible, but obviously they get enthusiastic and want to go off in other directions. (from Starlog by way of wikipedia)