Upon rewatching this scene with a lot of distance from it, it seems like what makes it work so well emotionally is Bertholdt. If you're writing something, you're always thinking about things in terms of "how do I bridge the emotional gap that's always present in a story?" I mentioned an example of this with the memory sharing device in Son of a Serpent, but this is another great example of it.

If you were writing this story with this scene in mind from the start, how would you make it maximally impactful? The feeling this scene needs to convey is betrayal, but betrayal is a hard emotion to evoke in others. The story itself is displaying a betrayal, but just because Eren feels betrayed doesn't mean the viewer will also feel that way, this is the gap that needs to be closed, the scene has to be constructed to viscerally force the viewer into the feeling of betrayal, and the way to do it is via Bertholdt.

Here we have a nice guy, passive, quiet, harmless, he's essentially a baby in the viewer's emotional model. The author underwrote him this way for two seasons, and then he decides to spend those two seasons here. As the scene develops and Reiner realizes he has to play his hand, Bertholdt is shown as unsure and insecure, unwilling to go ahead with it, as he had been shown up to this point, but then the actual action scene starts with Mikasa coming in and fucking trying to brutally annihilate Reiner, he half-parries, but then she goes for Bertholdt, and if you listen to the sounds, Reiner's is fleshy but kind of low, but when she goes for Bertholdt and cuts him, it's a massive critical hit, literally the sound that would play on a sword attack critical hit in a game, and Bertholdt falls, and the next scene... this, this, this is how you spend a character:

His eyes, his hands, his blood, his scream, all of it is perfect. Brutal and total violence against he who is most defenseless, against he who is most harmless, against he who needs to be protected, a perfect desecration, a visceral betrayal. This alone carries the emotional payload of the entire scene. Of course, in the story, Bertholdt is not defenseless nor innocent, but the goal of the scene is to evoke an instinctive emotion on the viewer, which is why the two season underwrite must be paid off in an action scene that moves quickly. The real thinking conclusion one would reach is one of confusion, of how Reiner/Bertholdt are conflicted, and so on, but these are complex ideas, and so the viewer must not be given time to process it this way, which is why this must happen in a scene that moves fast. And then Bertholdt is on the floor, gurgling, crying, screaming as his head was almost chopped the fuck off, Mikasa tries to kill him even harder, only to be shoved by Reiner, and then the very next scene is also Bertholdt crying, regretful, in complete pain, solidifying the previous emotional delivery.

And then the rest of the story continues, with Eren's final scream being the scene handing off the feeling of betrayal to the main character's POV. But it's important to realize that the feeling of betrayal was actually built emotionally on Bertholdt in the most visceral way possible. An extremely good bit of mixing the larger picture storytelling with the low level details of the scene's action writing. If you wrote the details of this scene any differently, if you didn't focus on Bertholdt, if you weren't as brutal to him, if you didn't have the "weakest" character suffering the most, the feeling of betrayal would have been much lesser and it would have been a worse scene. If you were writing the story backwards with this scene in mind from the start, you'd exactly underwrite Bertholdt as a character and have this happen to him here, it is one of the best solutions to making it maximally impactful, which is what you need such pivotal scenes to be.