I'm still not seeing the problem.
As Christopher points out, there are massive gaps in the novel chronology. And it's not like the novels couldn't be worked into the series as necessary. DC managed to work the third and fourth films into their comics continuity, and Marvel worked "The Cage" into Early Voyages
by retelling some of its events from a new perspective.
The advantage to mini-series is that they can mimic the same event-driven, epic storytelling that the novel lines deliver today. The advantage to an ongoing series with single issue storytelling and longer story arcs is that it mimics the episodic nature of the television series that has, to some extent, been lost.
I'm not trying to be dense by saying that I don't see the problem with coordinating an ongoing comics series with an ongoing novel series. If Mike Friedman could do it for a whole lotta years for DC with TNG
by carving out six-issue blocks within seasons for him to tell small and big stories, I've no doubt that Pocket and IDW could equally work out something that would work.