Will completing the Battle for Whiterun quest for the Imperial Legion in any way prevent doing the peace treaty thing? The wiki isn't crystal clear on the issue so I'm wondering if anyone has done this.

Just do the peace treaty first if your so concerned.

Umm not sure what happens when you proceed with civil war prior to Season Unending.... or what happens if you complete civil war prior to same. War sux anyway, not a hilight for me for sure.

http://www.uesp.net/wiki/Skyrim:Season_Unending