Disclaimer: I don't know anything about .Net, other than how to spell it, and I'm not completely sure about that.
It seems like one difference between a person using your file converter on their desktop and using it on a web server is that only a single instance will be running at a time on the desktop; a web page will probably have multiple instances, once per concurrent request. This seems like something you could enforce in software, and also something you could easily write into a license agreement.
Does IIS run with a graphical console on Windows? If it doesn't, and your desktop version does, maybe you could detect that?
Ultimately, though, if someone wants to get around your server/desktop distinction enough, they're going to; they could, for example, have the web server send the document to a desktop machine, and have the desktop send it back to the server. So, at some point, you'll have to give in and either ignore it or to say that's a problem for legal to handle.