It will be a problematic thing to do as it will require you to let the webserver run scripts as a system root. It is somewhat hard and requires a lot of thinking security wise about the implications of letting a web server do it.
But you are spared of all that thinking 😉 as your scheme is not practical as wordpress MU always runs as the webserver user and you will not be able to associate resource usage with different system users. To actually achieve what you want you will need to create separate wordpress install for each new user.
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