About the only possible solution here would be to special case ctypes to detect msvcr90 as a parameter (later versions of the CRT don't need it) and also whether another activation context already exists. We could also document the need for a complete manifest in the embedding docs. All of this really only affects 2.7, as later versions of Python don't necessarily suffer the same limitation (unless someone wants to load msvcr90 explicitly).

What functionality do you need that you can't get some other way (such as the msvcrt module)? Or is it just the uuid issue?