OK, this complaint has come up several times and several people have tried to answer it, but I want to see if I can clarify things a bit here.
In a recent WOG, LordR mentioned that he thinks the problem is that Joe is trying to account for actions of other parties and that is usually not accounted for in stories. I think this is the main disconnect. A lot of people are making assumptions that other factions will not react to Joe's actions, or will react in a certain way. Joe seems to be taking a broader outlook than most people are.
Cosmic covered most of these points, but let me see if I can illustrate this with an example. As usual, this is overly simplified, but I hope it gets the point across.
Realistically, Joe has two main options for dealing with the S9. Option one is he can wait for them to come to Brockton and strike them once they arrive, while option two is he could launch a preemptive strike. Lets see what the immediate consequences of these possibilities are.
For option one, the S9 would continue hurting people while approaching the city, then be wiped out by the CF. Let's estimate the effective casualties here between 50 - 100 people dead.
For option two, the S9 would get killed immediately. There would be some collateral damage, but as the strike would likely happen in a low population area it wouldn't be that bad. Let's estimate the effective casualties here between 10 - 30 people dead. There's also a chance of some members of the S9 escaping in this scenario, but for now, let's assume Joe prioritizes Jack and the survivors wouldn't be too much of an issue for the sake of simplicity.
At this point, option two would seem like the preferable option. It is also at this point I suspect that most of the readers stop their analysis. However, we have to remember that everyone in this story is an individual with their own goals, priorities, values, etc. and they all take action in their own interests. Any action taken by Joe will have ripple effects. With that in mind, let's go further into the analysis.
In the option one scenario, Joe's actions would shock most groups, but he could manage the reaction. It would be concerning for every major faction, but with the fact that the S9 had approached the city with the clear intent to launch an attack, Joe could frame his actions as a reaction to the S9's aggression. This fits in with most models of his behavior and while other organizations would be concerned, most would likely believe that as long as they don't provoke a reaction they can continue without Aperion deciding to intervene. Some groups might overreact, but most would simply strive to ensure none of their underlings or agents do anything that could provoke Aperion. Let's estimate the effective causalities as a result of this between 1000 - 3000 people dead.
In the option two scenario, Joe would have attacked the S9 before they approached the city. He could try to claim that the S9 were approaching Brockton, but the earlier he strikes the less plausible that explanation becomes. By taking proactive action, not only would Joe call into question the predictions about him, but many major organizations would realize that they might be his next target and likely panic. Remember that this takes place on Earth Bet, where there is no shortage of powerful, morally questionable (or outright evil) organizations. Most of those organizations would take drastic action to shore up their defenses, regardless of the cost. They would not know the threshold necessary for Joe to take action and many would have reason to assume they could be targeted. Even Joe claiming that the kill orders on the S9 constitute a contract, it won't help as there is nothing stopping Joe from taking another contract to eliminate them. In Brockton itself, the gangs would likely make as big of a mess as they could before fleeing the city, while organizations outside the city would likely do whatever they could to increase their numbers, regardless of the long term consequences. There would be many other ripple effects, but for the sake of simplicity, I'll skip them and estimate the effective casualties from this between 5,000 to 25,000 people dead. (Large range because of the wide impact and I still think I'm significantly understating the numbers.)
Based on this extended analysis, it now becomes clear that option one is the preferable option in terms of potential casualties. Thus, if taken in isolation from the reactions of the rest of the world, option two results in less causalities, but if the reactions of other organizations are taken into account, option one results in less causalities.
Once again, I would like to state that this is an overly simplified explanation with the purpose of explaining the thought process of choosing to wait for the S9. The actual dynamics of the encounter have a lot more variables, but the point of this is to illustrate the basic reasoning behind this choice.
From what I can understand, Joe is trying to take care of as many problems as he can discreetly before other factions catch on. Eventually, he will have to go all out, but he is reasonably trying to put that off for as long as he can so he can take care of issues and mitigate consequences.
(edit: SPAG)