We're currently working on a feature for CompleteFTP that will allow you to ban uploads with certain file extensions.
So you'll be able to enter *.pdf as an extension to be denied, and any attempt to upload a file with that extension will result in an error. Of course, this also requires denying rename attempts to banned extensions as well, otherwise people can simply upload with an allowed extension, and then rename to a banned one.
We are also planning on using deny or allow for each entry, so that (for example), you could ban all filenames and then allow only a certain extension.
If you have any feedback on this feature - certain requirements you might have, for example - please let us know as soon as possible.