I always scan 'em in the sleeves (PrintFile) for this very reason.
This is the way that I do it as well. I bought a cheap picture frame and use the glass to hold the negatives flat in the scanner. I wouldn't ever print from the scans, but it's a great way to check composition and especially facial expressions on portraits. I use the scans to determine which negatives aren't worth the effort to print which helps because I always have very limited time in my temporary darkroom.
If you can't answer a man's argument, all is not lost; you can still call him vile names. - Elbert Hubbard