Strictly speaking, the council has already decided not to go to war. Our characters operate under the banner of the Jedi Lord, who revoked his position on the council to lead a section of Jedi Knights to war against the Brotherhood.
I'm not entirely sure whether the Council and the Senate is respectively allied, but we still have to respect them and their position on things. They are not our enemy. We may not agree with their rulings, and we dont have to listen without the say of the Lord or the Council, respectively. But, shooting them down immediately will just cause problems