Er, not to nitpick much, but you do know that Mac Pro handles are part of a unibody chassis right? It's all or nothing - there is no separate handle you can affix to the case in any manner without welding (and I wouldn't trust that to pick up a 65 lb. machine).
Also, the handles being taken off to go under a desk would not impede any airflow at all. There is NO airflow at the top of the case. None. You could cover it with a rug and it wouldn't be more than a degree or two increase (as long as you didn't cover the fan ports on the back of the machine).
The handles were purely aesthetic, though building them into the case directly made it that much stronger and easily capable of deaing with the behemoth weight of the machine.