Or maybe you could "make an example" of the thief the first time, and the guild will leave your houses alone after that

I don't like the idea of paying protection money - seems a bit craven for a heroic TES main character.
Also, once you've gone through the process of getting your stuff back once, the novelty will wear off pretty quickly. So, IMHO you'll definitely want some reason in the mod that it won't happen again.
Actually: in Fallout2, when some guys stole your car, if you didn't gun them all down when you caught them, they were actually quite useful. Maybe you could have a choice at the end like that - either the PC murders the house robber, scaring off future robbers, or he/she manages to reach an agreement/do a favour for the thief, and will thus get favours back (including being exempt from house break-ins in future).
Maybe the PC tracks down the thief, who then tries to escape. In doing so, he stumbles into some daedra or something, and the player can save him. In gratitude, he promises to have the player's houses noted as off-limits at the guild.
This post has been edited by RobRendell: Dec 20 2005, 05:24 AM