Like a lot of collaborations, you will need a willing partner to make this work. If they are dead set against using Flash... there may be nothing you can do to change their minds. If on the otherhand, they want to work with you... then it's possible to find a way.
Use a video file format like .avi or mpeg, (mp4), not .mov to import into your video editing program... edit/render the video there to prepare for TV.
Pixel shape has to do with using square pixels (like a computer monitor) or using rectangle pixels (like analog broadcast TV).
So for example, a standard def, 4:3 aspect ratio. on a TV would be 720 x 480.... but do the math.... that is NOT a mathmatical 4:3 ratio, 720 x 540 would be. Expect that analog TV uses rectangle pixels rather than sequare, so it doesn't take as many pixels to display the same height as a computer monitor.... only 480 compared to 540 on the computer.
When starting to edit the program in your video editng program you will have the choice of working with square or rectangle pixels.
Best bet is to get the finish video stats from the people you are handing this off to, and match your final output to exactly those specs... just as you would (hopefully) do for any other job for a client. Don't expect them to change their ways for you... you get the specs from them and deliver that.
Many thanks for that answer my friend. Collaboration? I'd have never thought of that, being used to bending people to my shape with a will of steel and cold determination. But seriously, you're right of course. I see tradional Post Production houses going the same way as photo labs, now under threat everywhere from color printers and digital cameras. Their long-term investment is in convincing clients that only $15,000 worth of video-based post production is the solution to advertising because mugs with computers can't do the same job (ie. to produce a 30 second ad) for $2,000.
Since I posted, they have confirmed that a PNG sequence is how they would like it delivered but they don't seem to be any configurable options in Flash except native PNG, so I guess pixel shape will have to be sorted out at their end in their video editor. I'll be delivering a proof-of-concept today and I'll report back on its success (or lack of it). They have also confirmed the 1280x720 aspect ratio because they seem to think that everyone in the known universe has a wide-screen TV. And more and more often, I see letter-boxed TV commercials on my old 4:3 TV screen so it seems to be the future.
I'm surprised at the amount of digging I've had to do to get this far though, and many thanks again for your contribution. There's a ton of information out there about pixel shape, aspect ratio and stage size for different broadcast standards but surprisingly, from Adobe, there's not a lot of info on this. There's this: http://www.adobe.com/devnet/flash/articles/flash_to_video.html but that's last updated in 2006 and another excellent article at: http://active.tutsplus.com/freebies/applications/how-to-prepare-your-flash-documents-for-t v-broadcast/ but on the Adobe site itself, no clear advice or article. Flash is an animator's dream for simple production so its ongoing use as a TV production tool would seem to be in Adobe's best interests to develop. One article from 2006 does NOT an informed audience make.