But there's always the possibility of them deliberately doing some stories in the IDW continuity that are compatible with the novel canon as well...
I don't think there is a single IDW continuity. Some of their miniseries have contradicted each other. For instance, I believe Year Four: The Enterprise Experiment
and Romulans: Pawns of War
handled things like the cloaking device and late-2260s UFP/Klingon/Romulan relations and conflicts in incompatible ways.
And there already are a few IDW stories compatible with the prose; there's the New Frontier
comic and the Alien Spotlight
and Captain's Log
one-shots by Keith R. A. DeCandido.