Considering how much space and empty time there is to play with in the Star Wars universe, the only way the EU would even be effected is if episodes VII-IX directly contradict what happens there. If they simply choose to tell a story from the EU, or better yet, create a new story that doesn't contradict the EU, then nothing changes. I don't see why people are making baseless assumptions about the status of the canon when we don't even know anything about the story yet. There's a very real possibility that Disney will choose to cover some EU event (like fighting the warlords post ROTJ, or the formation of the New Republic) from a perspective we've never seen before, therefore making an "original" story.
That's what the rumors are saying already. The press release from Disney that says "Forget everything you knew about Luke, Leia, and Han as far as what happens to them after RotJ". I'm honestly hoping that's just hype and they think better of it. But if it's true, and Disney doesn't handle it right, it WILL piss off a lot of fans. Leland Chee, hopefully, is all over this already.