Dropping is not supposed to kill, only to separate the animals. Tame animals need to be slaughtered for any further use, if they die from the drop, the carcasses will be useless garbage. Dead wild animals are butcherable regardless of cause of death, but may be harder to auto-drop (i don't think they start infighting when crowded).
Going by the wiki, the only common domestic bird that's rated as a flyer is the goose, so dropping chickens would remain a valid separation technique. Birds don't really work for a sustained no-maintenance farm, though, because sterile or killed eggs will occur from time to time, and those permanently block a nest box until removed by a dwarf.
I like the idea of a re-setting water trigger, but suspect that pumps feeding directly into the chamber behind the door (or the door itself, if you don't rely on pathing, just on crowding/avoidance) would move the water too quickly and flood more area than is needed for the purpose. Adding a simple diagonal might improve the design substantially:
####
GD^X
##.#
#.##
#%##
#%##
G - Grate or other drain
D - "trigger" door
^ - pressure plate triggering on 0-5 water (or inverse, if you want the plate to be "on" when untriggered)
X - door to pathing goal or wall
% - pump taking water from south
%
The diagonal should remove flooding concerns. The drain should remain unused in most cases, but would prove valuable when the door stays open for a longer time, e.g. because critters congregate in the door tile.