i don't do box jumps much right now, but generally i just wore my vibrams when i focused on them. it does give you a lot of room between your heel and the floor to try and buffer the blow, but your actual foot can get sore.
i bet in the long run though, it would turn out bad....
if i incorporate box jumps now, i generally do them for height. as a result, i come down slow rather than jump down like you were talkin about.
if you're doing them for reps for conditioning or what not, you could try subbing in bodyweight squats to stop the repeated blow.