I think that it's just an outdated spec. Fact is, that 720p video conferencing is fine, but at a time when when our mobiles have better cameras it seems odd that the camera on a mobile or iPad looks better. Also - even though most VC apps won't use the 1080p, the video coming from them still looks sharper when downsized.
At this point, I don't know why Apple just doesn't put one in. I can only speculate that once the Intel-->AS transition is done and they have the bandwidth to turn their attention to updating the hardware as well, they will engineer a new chassis that can 'fit' a better webcam.
Until then this shouldn't be a dealbreaker for anyone. Just use your cell phone or other device with a better camera...