Urgh. How about installing the .py to a private directory (under /usr/share say?) and creating non-suffixed symlinks in /usr/bin. You could document that the user could/should prefix the /usr/share dir in their $PATH if they need to rely on the .py names existing, perhaps even provide a small helper script to support that if it is likely to be important. (assuming whatever might rely on the .py suffixes also relies on $PATH and doesn't hardcode /usr/bin/something.py in its entirety.)
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