Its been a while since I've played Fallout 3, I need to pick it up again since I felt disappointed with New Vegas lately.
I thought that event where Burke kills Lucas Simms in the beginning is a very interesting moment, designed to show the player the mortality of NPCs. We grow to like Simms for a few moments, even to meet his child, only to find him unexpectedly assassinated. This goes to show that even "good" characters aren't protected from death. Interestingly, its possible to save him using V.A.T.S., but most players wouldn't think to use V.A.T.S. in those few seconds, and even if you save him theres no real reward. The more interesting scenario is arguably to let Simms die.
As for your theory, well I find assaination organizations kind of silly in a game where most NPCs attack you on sight, but yeh that makes some sense.