So since this is meant to draw up a treaty for the Stormcloaks and the Imperials, will this cause me to be unable to join either side in the civil war? I haven't joined either of them but I'm at the quest where I need to start the peace council, I don't want to disable the chance to join either side though.

I don't think so, but I know it'll put certain quests in those questlines on hold until you've finished your business. Once you're done, you can continue either questline, but they do react to your actions in the meeting, which is pretty cool.

It's more a ceasefire.