This should be possible, although not easy, and if anything goes wrong you're stuck with the server not responding any more.
I'm not familiar with the necessary windows tools. I think you should install cygwin and some baic linux tools.
Then I'd try the following:
1.) create a new partition.
2.) take a working linux system (which should be able to work with the hardware of your server) and copy it to this partition. The best source for that would probably be a live distro, since these are usually configured to work with every hardware setting.
You should take care that a ssh server is configured and working.
3.) write a new master boot record (MBR) to the server's disk. This is probably the most tricky part, and I have just a vague idea of how to do that.
install-mbr (read the manpage here: http://manpages.debian.net/cgi-bin/d...8a&format=html
) should work for that. You must set your linux partition as the boot partition.
Then you're done. Reboot the server and pray that nothing went wrong.
If you really want to do that, you should be ready to read a lot of linux manpages and test it first on a local computer, so you can intervene if something goes wrong. However, it sounds like an interesting challenge.