I think it's just, those are "real world" things and not Jurassic Park movie dinosaurs, which we're used to seeing as bloodthirsty carnivores on-screen, but I still think that's a valid point. It's not like... say, a shark, which I don't think could possibly work considering their known level of intellect.
But where the movies are continually about (except TLW) how intelligent the raptors are, I don't see why presumably around a decade of Owen working with the same four, building their social skills, and them being supposedly that smart is out of bounds. And they still chased and killed people; they were by no means tamed or not dangerous.
I think at the end Blue had an understanding and Owen had an understanding of them, and his approach to Blue was respectful. I think she simply acknowledged that and realized that there's much bigger fish to fry, and who knows, without the Indominus in the picture and Owen not performing that gesture of removing the headset and so on, she'd have probably torn them all to shreds.
The tension and build is from the fact that Owen finally achieved that level of trust and respect, which saved him, Claire and the kids, and why the squad goes after the Indominus on Owen's command. By that point they pretty much were his "dogs" but with so many other factors worked in at the same time.
I just don't get it when people watch the movie and complain about how they were tamed, it's like, no, they weren't, and the logic for what happened was clearly there.