RPG Vault have posted part 4 of their Anarchy Online: Shadowlands Blueprint. In this part Funcom's Jon-Helgi Thorarinsson and Jørgen Tharaldsen talk about the new faction system in the upcoming expansion.
So far, there hasn't been any consequence for killing creatures from "your" side in the conflict. With the strong setting in Anarchy Online, we felt that something was missing in regards to consequences from "killing your own". With the coming of Shadowlands, we thus introduce a faction system. From now on, various NPCs will be more particular about players' previous exploits than they have been.
As a result of this, NPCs will have various ways of responding to players, depending on how much or little they like them. An NPC might attack a player on sight if he really dislikes him, refuse to talk to him if he is a bit ticked off, or agree to trade with the player if he is in relative good standing. More degrees of reactions are built into this system, as players will find out during their adventures.