NO. Dawnguard is NOT a civil war. Civil war has a quest that starts in two different places and has two different ultimate enemies. DG starts in one place, diverges a few times, and you still kill the same enemy. A lot better than the civil war in a lot of ways, but not in that way. The quests are pretty awesome for both parties, especially the radiant quests and side quests.
so it would be cannon no matter what.
TES has done non-canon endings before. Keeping the Umbra sword in Oblivion, for example, goes against what is said in
Lord of Souls. Killing Lucien Lachance before joining the Dark Brotherhood, as well, goes against the events of Skyrim.