The sneaking and ladder animations are always going to be controversial, but as much as I'm enjoying the more serious business of the MQ, I would be very, very sad to see them go. They're just those odd little touches that make the Divinity series what it is. I'd hate to see it taking itself too seriously, however dark the story is.
It's not about them being controversial though, regardless of how anyone feels about them they just don't belong. It's not because of how dark the story is - comedy can and will tell dark stories - it's because of the realism the game wants to convince you of. All of the text is trying to seduce you into believing these realistic and gritty rules of the world in order to make you care about what happens to the characters in it, and silly things like the sneak and other wacky character animations go against that and break any immersion the (amazing) writing may have created.
The wacky animations are not wrong. Larian just needs to decide if they're making a realistic game (as the story is trying to be right now) or a silly game (as the animations are trying to be) because no matter which one Larian wants they can't have both without hurting the players immersion.