No, because they form a natural equilibrium with their prey, and more importantly, because neither the predator nor the prey in those examples is sapient. Furthermore, I’m pretty sure if humans had any natural predators, we would be pretty morally justified in defending ourselves against them.
I don’t know if malevolence is even the best way to describe it in the case of mind flayers. Like I said before, I actually prefer to classify Aberrations as unaligned because they exist outside our traditional ethical framework.
Also, side note, let’s not pretend ceromorphasis is just a “breeding ritual.” It’s a violent invasion of a sapient victim’s body that destroys the victim’s bodily autonomy, and the existence of Neothelids proves it isn’t even an essential step in the Illithid lifecycle.
If you really want to get into it, I view Illithid
as essentially amoral beasts native to the Far Realm, whom the Elder Brains (which are absolutely evil) enslaved and turned to their own purpose. Which I’ve hinted at a couple times now with my comments about a campaign where you free the Illithid from the influence of the Elder Brains and then try to peacefully coexist with them.