Besides killing their king, are there any secondary leaders I can kill or quests involving complete genocide over them? My character hates them and want to completely wipe them out and turn them into nothing but a bad memory.

Nope. Doesn't matter how many you kill, or if you kill Madanach. They're always there, and they always hate you, and the hags always make more Briarhearts. Probably someone will make a mod to fix all that eventually.