Well, it ultimately depends on whether the file being uploaded is valid utf8, which apparently it is not.

If you can isolate the portion of your code at which uploaded file data is being read from the client, you should be able to put binmode STDIN, ":raw"; at the start of that portion, and binmode STDIN, ":utf8"; at the end of it (though perhaps setting it back to utf8 wouldn't be necessary, if the end of the file upload is also the end of the cgi transaction?)

For that matter, you might be better off having STDIN be "raw" at all times, and decode incoming stuff as utf8 only when appropriate. (I'm guessing that the actual file upload is taking place over STDIN -- and if I'm wrong about that, forgive me... file uploads are not an area where I have much experience.)