I'll distill my posts from elsewhere...
1) By generally avoiding settings which draw them. I don't often run a whole lot of games in setting based on media franchises.
There are a few I would consider running. Say, Farscape, which would pose an immediate problem in that it presumes that John Crichton is the ONLY man from Earth out in the cosmos. Which leads us to:
2) I have a general philosophy on "if nothing said that something didn't happen, then it might have." Further, just because common talk in a setting assumes something is true doesn't necessarily mean that what common wisdom holds is true. This is probably the biggest flaw with setting fanatics... they DO tend to assume that, until, of course, the author plainly contradicts themselves. Some fans aren't content to give the GM that much latitude. Which is too bad.
An example here is the common Wisdom that all Jedi but Obi Wan and Yoda died in the Rebellion era. Of course, it seems perfectly logical to me that there are OTHER Jedi hiding out... of course they aren't going to trumpet their presence, and some may have gone to extreme measures and went to extreme backwaters to hide out. Considering how kick-ass the Jedi are portrayed, it almost seems illogical to me that some wouldn't escape.
Anyway, some fans won't agree with me, and won't enjoy themselves playing in a game with my alterations, and I don't like playing in settings that don't give me enough latitude, and even I feel a bit dirty breaking with some canon. So I'd almost rather...
3) Make my own homage version of the setting which leaves me free of my own self doubt and that of others.
I have little respect for EU and none for FR novels. Though the chances of me running in the FR again are pretty close to nil, that latter is pretty much irrelevant to me.
In Star Wars, EU novels regularly contradict each other and any big details tended to get smashed by the release of new movies. When running SW, my general attitude is that EU is a great source of ideas, but nothing therefrom is considered to have really happened in the Caesar-SW-Galaxy unless I explicitly mention it has. Only stuff in the movies can generally be assumed to be canon (and that's less that absolute. Had
did shoot first.

)
I'm much less of a SW freak than some. It's a great series, but I see no need to devour every novel or collect every book about it. It's just one good movie series (well, the original) out of many. I don't memorize the setting with slavish devotion. I recently purchased the
Star Wars Complete Visual Dictionary. Next time I run SW, I will probably assume (and let the players know) that material therein can be assumed to be true, all else is fair game.
One EU bit I explicitly throw out: After the events of RotJ, Boba Fett is deader than a doornail.