No. WindowsRT will not demolish support for desktop any more than Android phones will. They are different devices aimed at different audiences.
The Windows team at Microsoft still considers Desktop to be the main focus for development, although obviously the marketing focuses on the "new" areas such as metro.
Also Microsoft has an explicit policy for application compatibility; applications should (in the absence of clear abuses of APIs) have a ~10 year life cycle.
If you're an early adopter of the Surface, then you'll have to wait for device manufacturers to catch up. Let's remember that Surface not only runs a different device driver model, it's also a different architecture, so you're just going to have to wait for the drivers to catch up.