Because you are outputting to the web, and not cutting a master to tape, nothing stops you from editing the DVCPRO HD 1080i50 / 1080i60 (PAL / NTSC) sequence preset to 1080p.
When you have a project open, edit the sequence settings so that Field Dominance is set to "None" and change Quicktime Video Compressor to DVCPRO HD 1080p25 / 1080p30.
I haven't checked in the Compressor app, but I know MPEG Streamclip can convert your 5D mk II footage to DVCPRO HD progressive footage.
Ideally you should test a couple of clips in both DVCPRO HD and PRORES 422 codecs and pick the one that is easiest on your system.