Once again, I recommend solving stuff like this by launching Maya (and most other tools) using a wrapper executable that configures the system environment variables etc. This lets you modify the python path at launch and put the .pyd wherever you want. You lose the ability to double click .ma files, but no one cares. The wrapper can be written in the language of your choice, including Python itself. Also, this lets people work on multiple projects on the same machine because their Maya/Tools environments are configured by the launcher, and almost nothing is set at the system level.