1. I have only gotten up to Diplomatic Immunity in the Main Quest. What happens if I finish the civil war BEFORE I finish the Main Quest? Does the person who replaced Balgruuf in Whiterun show up to the Council? Can I still trap Odahviing in the Palace?

2. Since Balgruuf was exiled.. can I still get the quest later on to obtain the "Ebony Blade" 2-Handed weapon?

3. Since Whiterun was attacked... can I still join up with the Companions and finish that quest line?

If you finish the civil war quest before Season Unending, there is no council. Just speak to the Jarl of Whiterun and he'll give you permission to trap Odaviing.

For Balgruuf, after he's thrown out, he can be found in the Blue Palace in Solitude, and you can get the quest from him there.

And yes, you can still join the Companions.

Anyone else? I could really use the help.

Noticed your edit asmodea, thank you. I was wondering mainly if Balgruuf just vanishes from the game. lol.

Thanks for the help!