A senate with representatives from each guild may work, except many guilds might prefer to go to a town where they could dominate instead of your town. A mercenary guild, for example, would probably prefer a guild town where the Governor is part of their guild. It would give them more of a free reign, and let them get away with illegal behavior.
Also, for the issue where you want to stop your town from becoming a guild town, the only way that I see is becoming an Governor yourself, and trying to be as impartial as possible.
