The cleanest way would be to scrap the Windows architecture and rebuild the OS from bottom. But their popularity will bite their back and asses: this would breake approx 3.5 million applications and even simple stuff like Virtual Basic.
It's quite a shame as Gates could use a free, non-viral operating like OpenBSD as the basis for a new Windows version. This can be done as Apple has shown and the superior security and performance features of OpenBSD would make the WinOpenBSD the best system in teh world.
However, this would have the negative side effect they we would never see Linux on the desktop as OpenBSD is much better in the security and performance aspects and with the fool-safe user interface of Windows XP added it would really be a killer. And the user interface should be even more improved in the next version of Windows as MS is very hot in reseach there.