I'm playing through the game again as a thief and just got my guildhall and was wondering does this mean I can't side with bodhi to get over to spellhold? Really wanted to try that out this time round but not if it messes up my stronghold quests.

----You just have to be evil every now and then.-----

<font color="teal"> Im pretty sure it doesnt stuff ne of that up... but I might b wrong.</font>

You could complete you stronghold quests before siding with Bodhi or Gaelan.
Once you side with Bodhi however all Shadow thieves will turn hostile thus ruining you stronghold quests.