We just recently used the MonoSandbox for Security reasons.
I don't know if it works with standard Microsoft's CLR, or if it is specific to the Mono implementation, but I think it works better than just a custom sanbdbox using AppDomains, and since the source code is open you can probably find a way to make it work for you.
The best documentation I have found for the MonoSandbox is here: http://www.mono-project.com/MonoSandbox