I think to be able to use Flying mount in the TBC expansion is unavoidable since it was one of the expansions main selling point back in 2006/2007.
What I believe you can do is however to:
1. Increase the level cap for the flying skill to lvl 70.
2. Increase the casting time for flying mounts.
3. Become dismounted while taking damage in mid-air (I don't remember if this already was the case).
The reason for these is to keep a healthy world pvp without a too big impact from flying mounts as we saw in the original TBC release.
The only negative impact I see is it will be difficult to do Mechanar, Botanica and Arcatraz since you need flying mount to enter the instances.
My opinion is I could manage without flying mount.