Sure you can, no one's stopping you
However, should the murder be witnessed it will still count as a crime and everyone in the guild hall will most likely attack you once you strike. Just keep the bounty under the 5k mark
Keep in mind that certain NPCs are essential(more or less) for other quests, not involving the fighter's guild. Like Eydis fire-eye(right?) for example, if you haven't killed her already.