I thoroughly clean the areas I pass through and do not leave any enemies behind.
I don't kill harmless beings such as spiders, bats, cows etc as they don't count as enemies killed, and there is no reward for killing them. I don't know if the merchants would count as enemies killed but I would not kill them regardless.
Crows doesn't count as enemies killed, but I kill them for the reward they drop. I don't know if snakes count, but I take their egg anyway. I take fish if I have free space in the inventory.