I think you think you have a problem you don't actually have. Pretty much any genre can be boiled down in the same manner you boiled down CoC. (e.g. Fantasy ends with "kill the baddie, get the reward".) Just because something is iterative doesn't mean that it also can't be varied. That said, let's try and work with practical advise to vary up the feel of your climaxes.
The tension of any good story, but more specifically any good horror story, comes in not knowing what's coming around the corner. More importantly, knowing just enough to know that what's coming around the corner is not going to be good. I'm sure you're already well-versed in the art of ratcheting up suspense as a CoC Keeper, but it's a good thing to just drive home and focus on for your game. Small hints, very little threat, keep that other shoe up in the air for so long oh my god why won't it just drop?
By the time they get to the climax it will be a cathartic relief even if it is still just flee or die.
And the payoff is the "oh crap" moment. Every CoC game/session should have an "oh crap" moment. It's the revelation, the glimpse into the truth of what is going on where the characters (and by extension the players) realize exactly how much trouble they're in and how outclassed they are. Cause the secret about CoC and its derivatives is this: that "oh crap" moment is the climax. All that running away, or fighting the cultist, or dying horribly, that's just the wind down, the after-effects, the epilogue. CoC at its heart is an investigative game where characters carefully delve into knowledge Man Was Not Meant To Know. So that revelation, when they finally discover something, is the setpiece that your session should be built around. All that other stuff is just the release of the tension of the last several hours.
Same s@*!, different day
But that's not to say that the ending stuff has to be the same all the time, it's just that it will often follow a formula(e). But don't be afraid to vary it up. The characters run away a lot? Stick 'em in an extendable hallway scenario right out of a nightmare (The thing is chasing you and no matter how fast you run you can't seem to go anywhere!) Note that this doesn't mean you have to kill them, just vary up their experiences. The characters always want to kill the big bad cultist? That guy was actually casting spells to try to prevent a summoning of a dark eldritch monstrosity, but he was so insane that he couldn't communicate effectively to the PCs. Vary up their expectations, keep 'em guessing. Cause ultimately that's what this game is about.