I would suggest using MPEG Streamclip to convert the footage to Apple ProRes 422(HQ) 1080i50 (shouldn't be any issues with sound sync, Streamclip is smart. And cool). Do your edit in that format. Export the finished file in that format.
And then in Final Cut Pro, create another sequence - with the SD DV PAL i setting that you need. Drop the finished file you exported from the first sequence into the second PAL sequence, click "no" when it asks you if you'd like to change sequence settings, and twiddle your thumbs while it renders.
I haven't worked much in NTSC formats, but I know that FCP handles different framerates with aplomb.