I guess I'm a little bit more hopeful - Lucas has acknowledged the books/comics/games/etc in his recent interviews as part of the universe, and he has exerted some amount of control over their stories before (usually just in the form of forbidding the killing of certain characters). Plus, there's at least some small precedent - I'm pretty sure the city-planet of Coruscant was introduced in the Thrawn books.
I'd predict one of two things. Either (1) he sets the movies far into the future after Episode 6, where the non-movie material hasn't ventured and the whole continuity thing is basically a non-issue, or (2) he at the absolute least uses the same names and very basic character sketches, even if the story is his own, and the main characters come from the following list of names: Jaina, Jacen, Anakin, Ben, Allana.
I think a couple of the book storylines in particular would make great trilogy adaptations and I'm holding out some naive hope for that, but the above two options I think are more likely.