Tricky one, but you can rig up a solution - I'm not sure about the final quality though.
First, you need to allow your iPad to use AirPlay Mirroring with your iMac as the target device.
To do this, you need to use a program like AirServer ($15 for a single user license) or Reflector ($15 again, but has a trial at least) or AirMac (Free, but not as fully featured) or AirPlayer (Similarly beta). Mountain Lion will have this feature built in, potentially.
When this installed, check you can get it to work - so ensure the iPad and iMac are on the same wireless network, and turn on Airplay Mirroring, pointing it at the correct host:
You should get a window displaying the contents on your Mac. Note, than even if you are using the top of the line iMac, the resolution of the iPad will still be too large to view without scaling, so expect some downscaling, either by the airplay protocol or the receiving app anyway, simply to ensure it fits on your screen. Given a choice, a neat halving to get the original 1024x768 resolution should suffice. The method of doing this will be different depending on which app you end up using.
Once you have a window running with out iPad screen in it, you can capture it with Quicktime. I note that you already use ScreenFlow (which I missed at first), so you can do this your own way, but for everyone else you can do it with build in tools like Quicktime. I am going to assume you are on Lion. Open up Quicktime Player, and go
File > New Screen Recording Hit the big red recording button, and you get the message
Click to record the full screen. Drag to record part of the screen Drag a neat square over your Airplay receiving window, adjusting as required to get a neat fit, then hit the record button in the middle, and do your stuff.
CAVEAT: Lots of things can affect quality using this method. Your wireless network may be slow, resulting in dropped frames or lag when recording. Your computer may be slow, or busy, resulting in dropped frames etc etc etc. Quicktime (if you use it) is already by definition recording a compressed video, not raw, and it's using an image source on your screen that is already displaying a video that has been compressed down from Retina resolution to something saner for desktop use. This method works, but the resulting video quality can vary wildly depending on your setup. You can mitigate to an extent with thoughtful configuration of your network and so on, or by using more expensive screen capture solutions that record raw etc, that but is up to you to decide how much quality you need. As it stands, the test video I put up was more than sufficient to be perfectly pleasant on YouTube.
Now, time to own up, I cannot get it to work with the free versions on
offer, but I have in the past, so I'm throwing the solution up anyway,
in case it's just me being stupid.
I have used the trial version (limited to 10 minutes) of Reflector though, and created the following video as an example, proving it can be done, but you may need to cough up for paid software to do so: