If you kill Goemoe (only possible in an unpatched game) you would not be able to complete the lizard council member quest, and therefore not be able to complete the game. Either Otho or Joram are required later, but you can safely kill one of them.
If your reputation gets too low, NPCs will refuse to talk to you and could turn hostile, resulting in missed quests, possibly essential ones.
Your best bet for being evil would be to be evil and sneaky, so as not to loose any reputation. Area effect spells that do not require a target, such as Poison Cloud, can be use to kill some NPCs without a reputation drop, by casting them near but not directly on the NPC.