I think really uninstalling is a bit much. Just deactivate it, and update it when the new compatible version of the mod come out? IF they cause conflicts, because as far as I know, Dawnguard only adds Legendary dragons, so I'd assume the only consequence you'll get is Legendary dragons who are actually weaker or of equal strength to your upgraded dragons.
Slightly off-topic: I don't have any of the dragon difficulty mods, so I wonder whether it doesn't come over as weird when the dragons start summoning skeletons/daedra? I don't know, it makes it sound like they've become full-fledged mages instead of dragons to me, and it's one of the reasons I didn't install it yet. I'm of the impression the dragons should just stick to the use of shouts, although much more varied than only the one shout they know in Vanilla Skyrim.
