Rule #1 - They cannot kill each other
In military or police operations, the rules of engagement (ROE) determine when, where, and how force shall be used. Ben and Widmore follow appear to be some form of ROE, as they've been shown to specifically relate to the use of deadly force against each other. Furthermore, Alex's death being described as a "change in the rules" could indicate that her status as a combatant had changed under the ROE. Similar rules or the same ROE prevents Jacob from killing MiB and vice-versa.
Also regarding rules: Kurtisray 14:29, March 5, 2010 (UTC)
FARADAY: What is important, Desmond, is what I'm about to say to you. I need you to listen. You're the only person who can help us because, Desmond... the rules... the rules don't apply to you. You're special. You're uniquely and miraculously special.