Applications can be made to run on either platform. IBM developed their ViaVoice product on Linux and ported it to Windows. The open source project GIMP (photoshop like graphics editor) has a version that runs on Windows. Even Richard Stallman's Emacs editor runs on Windows.
I don't think the Linux community would worry or complain about a MS-Linux. Given Microsoft's track record with software quality the other distributions would still be better.
Hampered by the original decision by IBM that nobody would ever want more than 640k of RAM.