While you're reading it in, just check to see if it contains any \r\n sequences:

  if (/\x0D\x0A/) { die "DOS files not allowed" }
[download]

If you're reading it a line at a time, you can do this for the first line or for every line, depending on how picky you want to be. If you're reading the whole thing into memory, using that pattern across the whole file will work.

Update: Use hex escapes instead of \r\n for better portability. Thanks ikegami and GrandFather.