How exactly do you do this, yes man mentioned that I could choose to ignore or exterminate a faction if I chose to do so. Thus far the only options I have gotten were to ignore them or if I did their faction specific quests, to accept them. Basically I want to exterminate the Khans, White Gloves, and maybe the Omertas. How do I do this, I realize I could just slaughter them all by hand but I was wondering if there was a 'story' way to do this.

Kill the leaders, mainly.

Then Papa will die.