Are you sure it's MPEG video in a Quicktime file? 'Cause that's pretty unusual...
If it is, is it muxed MPEG data? Get info in Quicktime, does it say "MPEG1 Muxed", or separate for each track "MPEG1 Video" and "MPEG1 Audio"?
If the data is muxed you should just be able to delete the Quicktime header, open the file in
HexEdit and do a search for 'mdat', you'll get two hits, delete everything up to and including the second.
If it it's separate MPEG tracks in the Quicktime file, you'll have to extract each (using QT Pro or the old Movieplayer 2.5 in Classic), save as self-contained Quicktime file, delete the header, and then mux them together (there are a couple of tools that can mux MPEG files, I think
ffmpegX can do it, and also
MPEG2 Works). I'm not 100% sure that this method works, but it should.