It's not a windows vs. linux issue; MC already has a functioning linux build that has some video capability. It's an x86 processor architecture vs. ARM processor architecture issue.
You can recompile it, but if you don't do optimizations and take advantage of available hardware acceleration, everything will run poorly (or not at all). Porting software to ARM is non-trivial which is why, for example, the ARM version of debian doesn't have as many packages as the mainline x86 version does, and why the windows version for the new Pi won't have full functionality.
FWIW I'm personally hoping that there will be an arm build, it'd be loads of fun to run MC on tiny credit card sized computers.