It does.
I was partway through the Civil war when I Was off to do some fort missions and couldn't do them.
Once the Main quest was complete I was able to resume the Civil war.
They emphasize throughout the game that it's just an Armistice untill Alduin is dealt with.
Well, at least that's something then, but I am kinda disappointed, I loved both the Empire and Stormcloaks but now it seems I have to choose between them. I hoped they could band together to collect real elven ears with each other. I join Stormcloaks, even though the Empire is the Thalmor's strongest opposition, General Tullius seems too much of a Thalmor bootlicker to me....
SPOILER(cant find the spoilter button)
Except on the moment of his dead, then he suddenly hates em