It sounds like you have a great opportunity, I would stop talking yourself out of it and pull the trigger.Also when you talk to them ask them why they are leaving and see if you can help them resolve the issue so they stay.

I am curious, how did this all resolve?  

Fortunately, Justice of the Peace Courts (the "People's Court") handle amounts up to $10K so it's pretty easy to file an action for less than $150 and it can usually be resolved in less than 60 days.

Being a landlord takes patience, flexibility, strong resolve when enforcing rules, and a long fuse.

It'd be tough to get the "best of both worlds", since the best of the single-lease-world is charging utilities, and less time spent managing - neither of which are particularly compatible with a student rental property. 

I would try to resolve their concerns but ultimately this is not one I would push.

I will get her to consult a lawyer to see how this issue can be resolved.

Still haven't quite resolved and answer to this believe it or not. 

Eventually (like once we marry, have kids and need more bedrooms; 2-5 years out), we will move into the main house and rent out the carriage house.There is already a poured concrete pad and hookups outside for an air conditioner, probably a compatible thermostat in home already.

I refuse to close on the property until these issues are resolved to my satisfaction.