Accessing .net app from runtime?

Hi - I'm not sure if this is the right place to ask  this; actually, I'm not even sure what to ask...but I'm hoping some kind person will take pity and help me figure out what I should be asking and where to do it.   

I have a runtime solution, and need to figure out a new software protection scheme in order to switch eCommerce Providers.  What I'm coming up against is the fact that there are very few protection systems that will wrap an .exe without having to integrate source code AND will work with eCommerce Providers that look for a web based license generation system.

What I'm wondering is whether there's some way using one of the FM interfaces to something like .Net, PHP, etc to use a source-code dependent system even though my runtime itself isn't compiled. 

What I'm imagining is some way to write some separate application that IS compiled, that would handle the licensing and that could communicate with my runtime to tell it whether an install is licensed, what options were purchased, etc. 

I'd appreciate any kind of input - suggestions on what is possible, what to read, what to think about.

Thanks!

Michael