Editing XDCAM EX natively is certainly an acceptable practice if that's the only format you're editing with. You however, are in a different situation. There's no reason to exchange highly compressed (and lossy) H.264 clips with another format (MPEG2) which is also highly compressed. This is just asking for a step down in quality because of a possible generational loss.
In this case I would create a ProRes sequence, drag both formats in, do your edit then export using current settings, which would be a ProRes movie.
- Don
Don Greening
A Vancouver Video Production Company
Reeltime Videoworks
http://www.reeltimevideoworks.com