A matter of efficiency maybe? The dude seems able to levitate and puppet around the corpses by just stuffing them with bacteria, but for controlling large groups from far away, maybe just having the bacteria manipulate the brain somehow like the Cordyceps fungus is more efficient.Why do they stop moving after being shot?
They are corpses moving with the ability of the momotaro, the literally can't die as they are already dead. The only thing to counter that would be to get the momotaro particles out of the dead bodies or simpli annihilate the body so he can't control them.