Back when the Prequel Trilogy came out they handled it with a lot of handwaving (Ruusan Reformation) or just straight up rewriting the canon around the decanonized stuff so it still fit. They've also had to do this yet again to accomodate the Clone Wars cartoon.It's a much smaller canon problem than the one Abrams sidestepped with alternate universes in his Star Trek, so I think they'll be fine.
Be interesting to see how the EU itself would deal with this.
So more of the same, I suspect. The EU's always existed on that kind of suffrage, that a major Star Wars production could bulldoze through its narrative logic at any moment, so I can't say they're that unprepared.