Considering that editing and then maintaining a python fork is a bad idea running the entire process in some kind of sandbox might be the best way - you wouldn’t need to intercept all system calls, just once involving access to other processes, filesystem, gui that isn’t yours and possibly networking. Sound and graphics could left unmolested beyond initial window creation, so there wouldn’t be much/any slow down. Problem is I know of no such software - its all heavy full virtualisation; and writing such a beast, multi-platform, would be a serious project. But thought I’ld mention this solution in case something pops up - never know what OS project might suddenly appear!
(And the extension of a game .mf file should surly be ‘.p3d’ right?)