Are you able to put the MPEG2 files onto the timeline and then render a movie? If so, I'm guessing you could simply render them to the settings you'd like and that would be it. Don't know how much impact this would have on quality of the resulting file, if any.
This opinion is qualified by the fact that I know very little (read: nothing) about field order in MPEG files since I've never had to concern myself with them. That said, I can't imagine any way of manipulating field order in Movie Studio other than to re-render the file in question.
If you have trouble using the files in MS, you can always use a great, free program called VirtualDub (from www.virtualdub.org). This program will open almost any video file and, simply by doing a Save As, export the file as a DV-AVI compatible with virtually any editing software.
The mpeg files that I had were captured from analog video tape's and then converted to DVD using another piece of software besides MS. Somewhere in the capture process the incorrect field order was selected, or the program that I was using set the flag wrong(I was using auto-detect).
The result was that when viewed on a TV, the video looked like it was recorded at 15 frames per second or had some wierd flashy effect when there was alot of movement. Everything looked correct when viewed on a computer monitor because the clips were converted to progressive scan automatically to match the computer monitor.
It took me a while to figure out what was going on and I now longer have the original tapes so I could not recapture them.
Here is what I done that woked.
1. import the clip
2. right click and go to properties and changed the field order setings to upper field first.
3. draged the clip to the timeline
4. rendered the movie.
I can now watch the old home movies of me when and my family when I was younger without getting a headache.