Yes, but the desktop experience and apps will still be a big part of Windows 8 unless you're running it on an ARM tablet. Microsoft will happily link to your native non-sandboxed app from their App Store.

http://www.engadget.com/2011/09/13/windows-8-store-to-sell-b...

Screenshot http://farm7.static.flickr.com/6209/6144024273_4b505de2fc_o....

I guess a big reason for locking down Metro apps is battery life concerns.