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."
Earlier, the Toa discovered that the Bohrok they had previously slaughtered were not only just doing their job, but were 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. Later, the Order of Mata-Nui trick a different team of Toa into bringing a rock that summons the Visorak to a volcanic island, killing all of them. The Toa are outraged that they were just duped into committing genocide, despite the reasoning of the Order that the spiders were Always Chaotic Evil.
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.