I love your 'solution', although devious, it's got moxy. Do you have WebMin running (root access)? You can change the server info file with webmin (set a custom header file). Another even better trick would be to put a redirect in your dns which redirects the request from netcraft's ip to a special perl script. The perl script could output what looked like a server line.
You will then be running a Mucrosoft webserver.

Feel free to forward your boss lady the millions of complaints from IIS virus haters everywhere. Da penguin's da bomb!
To clarify, redirect to a perl script which listens on
another socket locally. To mimic the http protocol.
It could be done but i wouldn't want to do it ;>