You will have to write your own CLR host, instead of relying on the IJW "it just works" .NET feature.

If .NET 4 is installed on the machine, this link describes how to do it: Loading the Common Language Runtime into a Process. With .NET 4, you can even load multiple versions of the CLR side by side in the same process (with restrictions though).

Additional information: Use CLR4 Hosting API to invoke .NET assembly from native C++