The holds you traded would affect the outcome of the war. Since you did the Main Questline before finishing the War, you would have had to do the Peace Treaty to get Balgruuf to help you. Events in the Dark Brotherhood questline can prevent you from finishing the Thieves Guild Questline-so always do the TG first. Events in the Main Questline can affect the War and vice versa. Many quests get screwed up that way-Missing in Action comes to mind. It's never a good idea to start the Civil War and then go do the Main Quest and come back.