We've just released CompleteFTP 8.1.2, which allows you to ban uploading files that have filenames matching the set filename filters.
So you can enter a filter such as *.exe , and any attempt to upload a file with a name matching that filter will result in an error. Files also cannot be renamed to have matching filenames, otherwise users could simply upload using a different filename and rename the file.
Multiple filename filters can be added, and one of two strategies can be chosen. Either the filters can be used to determine only the filenames that are permitted, or filters can be used to ban filenames, which is the default. The filters are site-specific, i.e. they apply to all folders in the site they are configured for.
Specific folders can have their permissions modified to ignore the filename filters. The non-Windows permissions show an "Ignore filters" entry which can be selected. This can be set for the owner, group or everybody.