GMs treading into licenced IPs is always rocky ground.
The first thing they need to do is explain to the players whether they're looking at running the game as close as possible to canon, as a "spinoff", or making major changes. If anyone objects, give up there and then.
I would never get a group together and say "we're playing Star Trek next week", get them to the table to play, and then proceed to tell them the Federation just failed, the Prime Directive has been recinded, and the campaign will be based around their pirate activities raiding civilian shipping and murdering countless innocents.
That doesn't mean I wouldn't run the game at all, it means I would ensure the players were comfortable with the idea before I did it.
When running with someone elses I.P., often it is best to start out as close to canon as possible, and ease in the changes slowly - that way you can gauge when you've "gone too far" and steer things in another direction before you risk alienating your gaming group.
Yes, you have to be able to put your own stamp on your game world, but not in a way that turns your players off wanting to play in it.
You don't have to tread so carefully that you're afraid to change a single detail for fear of someone not liking it - there's going to be some decisions that the players don't like somewhere, unless you're playing with half a dozen clones of yourself. Some things you can say "well tough, thats just how it is", but when you take the entire game world permanently outside of how a player envisions the world they turned up to play in, you've got to be prepared to make adjustments.
If you're intending to throw established canon completely out of the window, it's only fair to warn the group before you start. I usually prepare a "deviations from canon" booklet for players when I do this, so they can read about it before starting - first off, it's only fair they get to see they're not playing in the "real" version of that universe, and secondly it's stuff their characters should know anyway. I wouldn't want to play a B5 game, have a player announce they're heading to Centauri Prime, and *then* tell them that in this game that planet was destroyed ten years ago. If I told them before the game started and they were happy with the idea, then there shouldn't be any repercussions. Obviously I don't list the deviations from canon that their characters would not be aware of - you have to save *some* surprises
