If you put a fence at the base of the fall, mobs will still take their regular falling damage. Due to the fence taking up 1.5 blocks of space (this is why you can't jump over fences), the mob will hit the fence instead of the water breaking the fall.

This mechanic can be applied like this (not my trap - it's part of a world I downloaded):

Mobs spawn in this gigantic tower...

...and hit these fences. The water then funnels the items into the middle (which then connects to another stream flowing the lava you can see, to kill any mobs that fell through the middle).