You should be able to make use of the scripting runtime, but I'm not aware of much documentation for it.
Essentially you load the scripting runtime, tell it to inject objects into the runtime (so accessible from the script), and then tell it to run the script.
However the practical details are a lot more complex.
A different approach might be script components (you put the JScript into a specific XML format with a .wsh extension. You can then register this as a COM component and thus access via COM interop.