Crotchrocketslm
What is the monthly rent and what is the total amount they owe you?
It doesn't sound like you've got a contract with someone from the organization's signature on it, rather you've got a contract with your roomate. He may very well be in breach, but that doesn't mean the organization is.
Do you have a written lease? What does it provide for notice of leaving, and under what conditions may a deposit be returned? That's going to be your guide as to what they owe you.
I don't see any reason why they should be entitled to have the deposit refunded. If they want it, let them sue you for it.
If you want to recover anything from the organization you're going to have to hire an attorney to sue them (or at least write them nasty letters). You might be able to file against them in Concilliation Court if the total amount is less than $7,500. As part of your claim you're going to have to argue that the orgnization is responsible for your roomate's lease because he was acting as an employee when he secured housing.
Stearns County Concilliation Court
http://www.co.stearns.mn.us/departme.../conccourt.htm