MotW and 3:16

Okay, here's a question. Last week, we began a campaign of MotW, and we just about managed to bring the group together and frame the first mystery; and already now (after writing up some mysteries) I am wondering how a MotW campaign will go, with special reference to 3:16. Why 3:16? Well, that was for us "Planet of the Week", and the only strictly episodic game I ever really ran, so that's the basis for comparison; and during that campaign, we really slipped into the productive pattern of "it's about the mission", "it's not about the mission" (repeat ad destructum), discussed elsewhere specifically for 3:16. That pattern entailed that the first few missions were just that, straightforward missions with happy killcounting, and then every now and then, there was a session where the mission of course also took place, but really only provided a backdrop for other developments in party dynamics or in the group's engagement with the setting, such as when people tried to find out more about the 3:16, about Earth, etc. These "other" missions often followed up on missions which introduced some elements of doubt into the basic premise (i.e., shooting up a planet of pacifist rock-painting squirrels). Now, such shifts are obviously built into 3:16.
But what about MotW? The book (RAW) leaves little doubt that there could be anything dubious about going out and killing monsters. But how about a monster which happens to be the protector of a community ("kill the murderous golem!")? Or unique monsters which might be dangerous, but enrich the biosphere ("kill Alec Holland!")? Of course, nothing stops me from setting up such mysteries, but I was wondering whether just as in 3:16, it might be a "natural" development of a MotW-campaign that such grey areas show up, and muddle the hitherto straightforward campaign premise... Thoughts? Experiences?

Just like in AW you sooner or later come to the big question of "What the hell happened this one day fifty or so years ago?" - sorta same way your campaign in MotW will move and paint the white spots as well. While team may contain Expert, many things that are _true_ about the world of supernatural are established in play - and some things even those in the know are not privy with at start. You paint the world - the knowledge(who they are, how this work, is there a God, or he has left the building, how werewolf-vampire relationship work, what do daemons truly want, and so on), history(like in my game there was a really big piece about WWII and believe me, daemons and vampires were there in the deep), geography(what really is this Bermuda Triangle, is there really a Shambala), and etc and etc.

And.
And. Not a single *W game can be not about people. Society. How you, strange crazy folks, find your place in this society. How society is composed, can there be a balance between vampires and humans, are there any "good" fairy or daemon and so on. Yes, on start there can and very well will be this period of "let's kill every monster we see"
But then you see that some monsters you can't kill because they're part of the society. Some can be killed, but social repercussions can be devastating. Chances are this creatures has been here for a long, long time, and you can't just "go and cleanse the earth" with your two shotguns and a pitchfork.

To help with the social part - work the game around some concept beyond killing. Agency is a very good start. Reporters, too. Initiate is taught about how this world works, expert learned it the hard way - they all care about the situation beyond immediate consequences. Like "should I kill this young and stupid mage girl who just almost fried her boyfriend's brain trying to make him stop using drugs? What will she become in a couple of years? Can I afford to not interfere? Who can be trusted with teaching her, if I can't do it?"

I can't add anything to what Guns_n_Droids said - that's exactly it.

I find that most MotW games start out very episodic, then (as the Keeper creates arcs) get more and more focused on ongoing problems for the hunters.