In BIONICLE, Kiina and Ackar are initially reluctant to attack the seemingly-humanoid Rahkshi, but have no problem chopping them up when they realize "They're just slugs in armour."
That's only the most recent example. Earlier, the Toa discovered that the Bohrok they had previously slaughtered were not only just doing their job, but actually transformed Matoran. They're suitably shocked at this, although more at the Body Horror than the killing as Bohrok have been proven to have no inherent intelligence.
Earlier still, the entirety of the Visorak arc. The protagonists are changed to beastmen, which they find horrifying, but they have to learn to appreciate their new forms for what they are before the Deus ex Machina will turn them back. There are also the Rahaga (who are eventually revealed to be transformed Toa themselves) that go around trying to save the wildlife from the evil army. Said evil army is made up of Giant Spiders whose name means "stealer of life" in their own language... and the arc ends when one of the protagonists disbands the army and points out their former ruler was a tyrant. But not before his partners kill a bunch of them.
Somewhat related, but Matoran (at least the ones on Mata Nui) have always found that harming innocent wildlife is wrong, and some actively treated injured animals that the Toa had defeated.
Actually, it's recently been revealed that the Great Beings never meant for the Matoran universe to become populated with sapient creatures. Which has Just a Machine connotations...
Viciously averted with this video showing people torturing and inadvertently killing robot dinosaur Pleo to show off that it actually had pre-programmed behavior for this kind of thing. Cue scores of angry YouTubers likening it to animal abuse and wishing... unfortunate circumstances on the two people in the video..
