I don't see how you are going to achieve this on the server without actually invoking a copy of Word/Excel/PowerPoint on a Windows box somewhere. And then, aren't those files going to need the fonts embedded in them in case the machine that you are running Word/XL/PP doesn't have them installed?
Lastly (sorry to be a wet blanket--it really is a great idea), there are tons of job options to be set in Distiller, and sometimes you want different options depending on the contents of the file.
This is a tough problem--it seems like it would be easier just to convert the file to PDF before you upload it.