serious compositing can only be done on progressive footage. Deinterlace on input to get progressive footage with twice the framerate (50i->100p) then do the compositing, and finally re-interlace. I would recommend de-interlacing and re-interlacing with ffmpeg, and using an intra-only intermediate codec (DNxHD or prores) or individual frames
It is what I do at the moment, 25i in ----> 50p.
I was hoping that on export I could re-interlace to save me an extra step of interlacing outside of Natron.