Now the sequel trilogy is going to invalidate a vast swath of the EU
Says who? No one knows what the new trilogy will be about.
Says common sense. Typically, tie-in novels and comics are read by maybe 1-2% of the filmgoing or TV-watching audience. Nobody's going to avoid making a movie the way they want to just because a tiny fraction of the audience will find it contradicts something they've read. Tie-ins just aren't that important in the grand scheme of things -- and I'm saying that as a tie-in writer. As a rule, tie-ins follow the films' lead, not the other way around. The canon can draw on ideas from the tie-ins when it's useful, but it can also contradict them when it's useful, because the canon always takes priority. One shouldn't expect any canon to be constrained by its tie-ins.
Besides, we've already seen The Clone Wars
contradict the EU where its portrayal of Mandalore was concerned, not to mention contradicting the previous Tartakovsky Clone Wars
animated series. Heck, canon contradicting tie-ins goes all the way back to The Empire Strikes Back
-- since there was an early Marvel comic with a flashback alleging that Obi-Wan had once gone on a mission with both
Darth Vader and
Luke's father. Not to mention the stuff in Splinter of the Mind's Eye
that was pretty much ignored in later films. Heck, the prequels even ignored or contradicted some details from the original trilogy, and the special editions of the OT changed things in the movies themselves. Even canon isn't immune from contradiction, in SW or any other long-running fictional franchise. It's always the prerogative of new works to overwrite elements of earlier works.