bjorn is right - in an unmodded game, you won't be able to side with Bodhi at all if you're a Thief, so there's no reason to get rid of the Guild unless you really want to.
I can't remember which MOD let's Thieves side with Bodhi, but if you want to add some extra quests to a future game (I don't think it will work if you already have the Guild), try out the Expanded Thief Guild MOD at...
http://www.fortunecity.com/boozers/winelodge/79/
It adds a few more quests & interactions & is bug-free as far as I can tell.
- Imrahil