Open the file as is in MPEG Streamclip.
Export to a non lossy QT format like Animation. (File export to Quicktime, select animation as the codec)
Open that in QTPro.
Rotate and save in a reasonable format, H264 with a bitrate of 1400 will do a good job.
You cannot export MPEG 1 or 2 at all from QT and not lose the audio so you will have to convert to QT with Streamclip to get a workable QT file that you can edit in QTPro.
Since it will be gigantic you need to compress it so it can be submitted, if they handle H264 then use that, if not use MPEG-4 and a 2500 kbps bitrate.
Note MPEG-1 looks pretty lousy most of the time, and a lot of Youtube clips look pretty awful too in Flash due to low bit rates originally and upscaling bigger than 320X240 (MPEG-1 standard) so this should look no worse.
I don't rotate clips as a rule, but when it is open in Streamclip have a gander at the options and see if you can rotate and save in MPEG-4 and all in one step. I know you can crop the size, so rotation, maybe too.
