Not as bad as it sounds at first: Microsoft provides free anti-malware tools (Microsoft Security Essentials stand-alone, Windows Defender included in Win8, and the Malicious Software Removal Tool through Windows Update). If you use these tools to remove the Sefnit malware, it removes the old copy of Tor that malware installed as well. It doesn't touch any newer self-installed versions.
The Slashdot post is terribly misleading. Microsoft appears to have deleted installs of Tor that the botnet themselves installed, which was a specific version. Subsequent versions of Tor auto-updated, so it's not like they're just deleting every single version of Tor off every single Windows machine.
The discussion seems to imply that this wasn't malicious over-reach by Microsoft. Rather the version of Tor was out of date and hidden in a peculiar location on the computer, possibly as a signature of how the bot kept itself hidden from the user.
Whether a corporation should have the power to do so is perhaps debatable, but this seems to be what the Malicious Software Removal Tool was made for.
Here's their own writeup of the cleanup effort: http://blogs.technet.com/b/mmpc/archive/2014/01/09/tackling-...