Having thought a bit more about this, and I'm feeling more optimistic. It's obviously jarring to see the license leave Dark Horse, where it has been before I was even born, but there's no reason to assume that Marvel will do a bad job with the comic side of things. This will be a great time to go back and read the old Dark Horse stuff and reflect on it all. I would echo a few other posters that a lot of our love for the DH stuff is colored by rose tinted glasses. They did some amazing books like Book One and some of the recent minis, but the DH line also suffered from weird editorial choices and from trying to play catch-up with the movies. Remember how the original trilogy was clearly setting up the Jockeys as the next big bads, only for that to get thrown out in a little one-shot? That's not at all to dismiss what Dark Horse did with the license, and I still love a LOT of the old books, but we shouldn't pretend everything has been perfect. And given how much of the recent material was stewarded by people like Brian Wood, a change isn't necessarily unwelcome.
As far as what Marvel does with it, I think it's accurate to say they'll go the Conan route IE a separate line of books in their own continuity along with separate "in continuity" crossovers with the main Marvel universe. I don't think Marvel or Disney are dumb enough to dilute the horror aspect of these brands, so I am not worried (at least not yet) about them being PG-13-ified. I also can't be mad that the inevitable crossovers, given that DH and DC have been doing them for years. I'd much rather read a Venom vs Aliens book than AvP vs Batman and Superman again. And honestly, I'd be lying if I didn't think it would be cool if Marvel's big 2021 event was "Alien and Predator invade the Marvel Universe." Give it to the creative team that did Absolute Carnage last year, or the Immortal Hulk team, and you could have a great little horror event. Marvel did it with Godzilla back in the 70's and it was great.
I just hope at the end of the day that this leads to more Alien and Predator comics. DH has definitely upped their regular output in recent years, but I still want the promise of an Alien ongoing fulfilled.
My only real question is what become of the Prometheus side of things. Will Marvel and Disney abandon it if they don't move forward with Scott's last movie, or will they allow that story to be told in the comics?