Hi Nikkilouise, I'm a Nikon user so can't offer an opinion on Canon lenses but I will say that if you're using a shutter speed slow enough that you need IS then it's too slow for birds in flight as you'll get blurring due to subject movement.
I have the Nikon 80-400mm VR lens which is broadly equivalent to the Canon 100-400mm IS. VR is "Vibration Reduction" - the Nikon version of IS - and I very rarely, if ever, switch it on. This thread explains why not:
VR (or IS) - Is it worth it?
In your shoes I'd be very tempted to go for the straight 400mm lens and not worry about the IS. Ollie has shown what it can do in a skilled photographer's hands, his in flight shots are some of the best on WAB.
Dave P.