Tablets != desktops...
Microsoft have tried running the Windows interface on tablets and IT DID NOT WORK. Not even with a pen interface to allow pixel accuracy mouse pointer resolution.
Apple proved that tablets are more smartphone like than desktop like and built a dedicated iOS to run it. Apple are also proving, with Lion, that desktops are not tablets -- some of their changes are completely maddening when tablet techniques are implemented on a desktop (e.g. Launch Control, Mission Control, intrusive animated page scrolling, daft full-screen operation, cheesy application changes in Mail and iCal...).
You need two interfaces. One interface for tablet mode when you've fat fingers, no keyboard and portrait layout. You need another interface for the desktop when you have fixed widescreen layout, mouse, no touch capabilities, a decent keyboard and possibly multiple monitors.
Microsoft are stating the bleeding obvious; APPLICATIONS BUILT FOR ONE PLATFORM WON'T WORK ON THE OTHER. Or at the very least they'll be very sub-optimal as user interfaces and even to the level operating system support with CPU capacity as battery life matters when in tablet mode.
Therefore just cut the cord: Windows applications simply don't exist in the tablet space, so it's a clean slate for them to start with.
Tablets represent a long-term structural change in the personal computing space. Microsoft, with their excellent development environment (there's simply no comparing iOS' Objective C with Microsoft's Dot Net) are in a very strong position if they can only get their act together.