It gets really complicated when you have download sites that are allowed to direct link because they are pulling in data from your PAD file. You can't really add just the download sites to a whitelist because in many cases you don't know all of them if you have your PAD file submitted to a PAD directory. Plus, even if you could whitelist them, that list could change daily.
The alternative is that you could do what you said for all other downloads, and have a separate file location just for those sites using your PAD file, but that could easily double the disk space needed to host your site if you end up needing to use 2 different copies of the file and that might not be possible for an author that has cheap or free hosting with a small disk space allowance or his web host only allows static html pages. (no cgi, php, or whatever)
Also, meta refresh may not work if the user has that disabled in his browser, and many do. Almost everyone I know on dialup has it disabled because it gets quite annoying on sites where you are trying to load a page and it keeps refreshing before the page is even halfway loaded.