The problem with the Thrawn Trilogy is that it's too close to Episode VII that it's going to have to be recognized in some way, which is why Disney is doing this whole removal of the EU in the first place. Disney doesn't want the baggage of already written stories, so expect that even if key story elements and names are kept that they'll be changed/altered in some way.
Like I said before, popular characters and names will probably stay, but they'll more than likely be changed in some way to better accommodate the movie franchise. So expect Mara Jade to be recreated into a different character that will better represent an actress that will play her. She'll either be changed to look more like an actress (i.e. - no vibrant red hair) OR she'll be entirely rewritten into someone else that will have nothing to do with Luke so she doesn't have to show up in Ep. VII at all and have her initial appearance altered. JJ/Disney might not even want Luke to ever be married, so background story elements for her can be changed, even. Again, excising the EU and changing the EU are gonna come hand in hand. Just cuz the Thrawn Trilogy comes before Ep. VII doesn't mean that it won't get in the way of whatever JJ and Disney will want to write for the new movies, and it'll all be altered accordingly.
Couple of things wrong with your post.
1) Thrawn triligoy is not CLOSE to the new film. it takes place 9 years after a new hope, which puts it roughly 6 years After Return of the jedi.
Which sets it roughly 24 years before teh new abrams picture.
2) Disney is not " Removing the EU in the first place". that's Ot purist fanboy rumors. were this the case, tehy wouldn't have bothered forming a comittee to do it. They are fixing the canon hierarchy, which is a damn mess.
Currently there are several tiers of canon, with different names, which basicly goes like this
Movie only canon
Movie + Tv show canon
Movie + TV Show + Novels
Movie + TV Show + Novels + Comics
Movie + TV Show + Novels + Comics + Games
If something is contradicted by another tier of the hierarchery, the higher tier is considered " More official"
What disney is doing is saying " This is stupid, and overly complicated. Leiland Chee, you and your team fix this, streamline it, throw out and/or fix things that contradict it, and give us an OFFICIAL HISTORY we can use for the new films. when you're finished there will only be one " Official Canon, and everything NEW that gets made must be approved by you and your team, and is official canon going forward." No, that's not supposition, nor guesswork, that's what's been OFFICIALY STATED that they are doing on a few occasions already.
what we don't know is what, specificly is getting tossed out, what's getting amended, and what's staying intact. I'm willing to wager, however, that the farther back the material is, the CLOSER it is to ROTJ, the less likely it'll see many, if any changes.
Now, that's not to say they might just say " **** it, hit the reset button" after all, only that your information is a little wrong.
Beyond that, Star wars has a huge legacy, and has a much tighter leash than the one that is on Star Trek. You CAN BET that JJ will be reigned in, if what he wants to do is too beyond the scope of what has already happened.
It's also worth noting that it's said that JJ is an old fan of the Star wars Novels ( Rumor) so take that for what you will.
final thought. Disney owns Lucasfilm. They also own marvel. How they have handeled marvel is a pretty good example of how they will handle Lucasfilm, i'd wager.
Kathleen kennedy is the current head of Lucasfilm. so what she says, is what goes. YES, she has to answer to disney, but As they have shown with marvel, disney knowns not to mess with the geese that lay golden eggs. Provide a budget, and an outline, let the company do what it does. Collect a paycheck.
