I don't mind. My groups usually try to avoid running into the canon characters on the other side unless we plan going in to toss what happened in the movies and EU out the window like the setting where we had Palpatine die because Anakin got held up in traffic on his way to Palps office in ROTS and our party was added to the force sent to arrest Palps. The Clone Wars were still raging 8 years later, we did several campaigns in that one. That one turned into a 4 way war between the CIS, Republic worlds that rebelled after Palpatine's death and the pardon of Mace Windu, the main Republic (Which actually included Anakin since we felt he would have followed Padme's lead and she would have stayed with the Republic), and a resurgent Mandalorian Sector (This started before The Clone Wars Cartoon second season threw out pretty much everything previously established about Mandalore's role in the war.)
Groups I've been part of have worked with several canon or EU characters though. We've been rebels at Endor, or NR forces at the taking of Courscant several times, part of the Bacta War a couple of times with different groups, and members of Luke Skywalker's, and Han Solo's fleets in the GCW