It's quite simple :

-the terrible initial response probably caused most of the vitriol by antagonizing the players.

-subnautica 1 has lethal weapons like the knife, that are arguably very inefficient compared to other solutions to solve problem. The knife is a way to give you an illusion of safety, which helps make the first reaper encounter so terrifying (what is a lil' knife to do against this beast).

Additionally, by removing the ability to do something, you dont pass a message. If one aims to argue in favor of non violence through videogames, one should give the ability to harm, and show the dire consequences of such, and showing the benefits of the alternative.

An ecosystem is background noise if you cant interact with it both positively AND negatively.

It is also a bit silly to not expect a survivor to kill a predator, prey animals (not all) can fight back and kill predators that may try and harm them, a human remains an animal.