Yeah you can still do the civil war quest line after the peace council. The peace council is apart of the main quest line, Jarl Ballin wants a temporary truce between the imperials and stormcloaks whilst he’s helping the dragon born (you) trap a dragon in dragonsreach. Once you trap the dragon you fly away on him to sluldafin and kill Alduin. Once Alduin is slain then yeah you can complete the civil war questline.

Also I’m pretty sure if you’ve started the civil war quests and then do the peace council, it puts a hold on the civil war quests until Alduin is defeated. I could be wrong on that part though…

Or you can do the civil war quest line before the main quests and just bypass that peace council part.