What's the end goal? GIF can only have 1bit alpha, so you'll end up with bad masking, if you're trying to use the animation on top of something else that's unknown. MPEG4/H.264 does support an alpha channel, but you may have difficulty generating what you're after.
If the end goal is for use on the web, CSS3 animation can do what you're after with just the two images.
If the end goal is for use in an iOS app, then again, there's ways to animate using CoreAnimation that will only require the two sides as individual PNG images.
If the end goal is for use as part of a video, then you may be better off doing the 3D rotate within Final Cut Pro X or Premier or whatever you're editing in.
If the end goal is for use in a presentation, then Keynote can do the card flip already.
So I think the best solution may be a totally different approach. If you do want to animate within Illustrator or Photoshop, then you'll probably have to create each frame individually — a painful and slow process that will make things like getting timing and easing right very difficult. For example, you may want to have the animation start slow, pick up speed, then slow down near the end. It's easy to have an ease-in-out timing curve with CSS3 animation or CoreAnimation, but harder when you're editing by hand.