Thanks for the tips guys. I've now tried both methods and repal seems to do the best in this situation but it's not perfect.

After some deliberation, I've decided to just leave it as it is. I'm going to be encoding these and putting them on blu ray so I think leaving them in an NTSC format will be best for compatibility and it doesn't look bad during playback to me. If the fields weren't blended I'd probably invest the time into converting them back to PAL.

Btw, I noticed a couple of scenes with really high motion that QTGMC couldn't handle with default settings. I changed search to search=5 and searchparam to searchparam=32 and it worked just fine so it seems the default motion analysis settings for mvtools isn't quite robust enough to catch really high motion. You can get search=5 if you use the placebo preset but searchparam never goes over 2 unless you set it manually. To me this means if something moves more than 2 blocks in between frames, then it is not processed properly and you get ghosting or blurring. Maybe I'm misunderstanding the documentation. Otherwise, qtgmc is a really great tool imo.