Here are few tips to help along with the above.
- It is safe to kill dogs (or any other animal), you cannot kill human enemies with weapons in Snakes possession, these count against you.
- You can "kill" unconscious/sleeping enemy soldiers by dropping them off cliffs, into water or into their own pit traps in cetain areas, as the game does not acknowledge those as kills in a playthrough at the ranking screen. Only kills from weapons Snake can use will be registered.
- Also kills from soldiers who have eaten poisonous food or have been attacked by poisonous animals you throw at them do not count.
I found this info especially useful for my FOXHOUND rank playthrough.