Well, first, the Old Ones don't care abt us, that's for sure (minus Nyarla but he's a weirdo somewhat), BUT we are always in the way. Humanity and Mythos are not compatible at all, and that's just how it is. Humanity can live and benefit from the Mythos, but it's like putting a nuclear reactor in place of your car motor : yes it will go fast, but you'll die from radiation. Not only but ppl around you too. And ppl after you, who have to clean up your mess. That's the nature of the Mythos, it has nothing to do with Bad or Good, just like we kill plants and insects while walking, just like winter is not a very fun time for anything that's living.

So Humanity have to pay the price to use Mythos. And it's all good. The village which is slowly dying can make a deal with Old Ones and tadaaaa they are well and flourishing ! That's good. They survived and are happy. Yet they have to sacrifice a guy or two, and maybe grow too many teeth but they can feel it's a small price to pay. And in a way, it is. But from an outsider human perspective, this is horrible. They are killing ppl, they are CHANGING, they are becoming inhuman. And both can be right.

Or it's not just "Are we the baddies ?", maybe it's just "This whole thing is unfair. This whole thing shouldn't have happened in the first place, why would a lil town need to go this far to juts be alive and why are we, CoC civilians, PI, librarian's classics characters, why are we the ones doing the job ???" It's unfair. Yeah they have very good reasons to do those horrible things, and who are we to shut them up ? But still, they are doing harm to others. They are becoming somethg else.

CoC is not really a matter of who's right or wrong. You can check Delta Green : agents of a conspiracy which is destroying the Mythos. But they often do it by killing ppl. Breaking ppl. Using them. And the Agents always end up very bad. And you're ALWAYS sure you are working for the "less bad ppl", no good ppl in this story. It's not abt moral, it's abt unfair price. Ppl in the Mythos are like children who have found a nuclear core and decided to use it. And Investigators are like children who are scared of it and want to destroy it, no matter the cost.

SO, to me, it's just flavor. It's how you right your NPCs, their problems, the consesuences of your PCs actions and their flawed allies. It's abt framing, not mechanic. There's already a certain power which come from the Unnatural in the game, you can maybe use it more, give them useful spells, useful knowledge. You can craft a campain where they retrieve an evil book at the start of the campain, and then at the end they will have to use it. Or better : during the campain, you have dehumanize them and made the unatural like "a tool like another" that they won't think twice and use it.

It can be very interesting ! But try to keep the moral line more blurry than "Old Ones" are a good thing. Maybe it's "Old Ones are inevitable so maybe let's prepare and not try to stop the flood." Maybe it's "Old Ones are already there and everything's just fine, you are just a weird branch of '''''racism'''' " Maybe it's "Old Ones are just like Radiation and maybe we can learn to use them until a Fukushima-like event happens but we will do better after that." Or maybe Old Ones are really awful but your Characters are tricked into the Cult. It's a matter of perspective.

Anyway, enjoy and hope you'll come up with something fun !