I've ran both before, but you lose out on damage and utility (plus Kidomaru lowers resistance and Kimimaro is mostly Taijutsu damage). I've also fought against both, and I just focus their main or Kidomaru first, knowing Kimimaro requires 60 chakra for his mystery and it doesn't do that much in Arena anyways.
I'd prefer something like Kidomaru, Kabuto, Tobi, Fire main. Have the threat of a tank that gets tankier with a stacking shield as well as the damage from Tobi and ignition.