Let's bring this back to particulars.I haven't ignored it at all. I'm merely unconvinced that the fact that mindflayers need to kill humans to live and propagate makes them objectively evil, and restating it repeatedly doesn't make the argument more convincing. It does make mindflayers enemies of humanity, yes. It makes it prudent for humans to kill mindflayers on sight. But mindflayers have apparently zero choice about their need to prey on humans, so that in itself is insufficient to make them evil.
(also, given that mindflayers rely on humans for sustenance and reproduction, they aren't a complete existential threat to our species since they'll die out without us)
There's definitely an asymmetry, agreed. I'm not sure it's particularly moral, but if you insist to read morality into the asymmetry then in most moral systems I'm familiar with, and evil act committed due to the need to survive is less objectionable than an evil act committed based on the expectation that the target of the evil act will do bad stuff to you in the future.
Furthermore, if we apply the reasoning that the nature of the mindflayers make them an existential threat to humanity (agreed), and that this justifies humans attacking mindflayers on sight and exterminating them as a species (also agreed), that makes human an existential threat to mindflayers. If exterminating those who are existential threats to you is inherently good or evil, then that makes mindflayers and humans equivalently good or evil (on that count, at least). If there is some sort of differentiation due to mindflayers having no inherent choice while humans are not strictly required to kill mindflayers (i.e. they are obligated by morality, not by satisfying base survival needs), that would tend to make the mindflayers slightly less evil than humans I'd think - at least normally we tend to ascribe less moral approbation to evil deeds done when there is no choice, versus once committed while alternative options were available.
The bottom line is that we agree that the mindflayer eats brains because it has to, and that's as far as it goes. In my eyes that is as morally neutral as any other inalterable fact of nature, that is to say neither good or evil (so maybe it's an evil to be put at the feet of a theoretical creator deity). If we must apply morality to inalterable facts of nature, we can't (at least from where I sit) start with the conclusion ("we are good while they are evil"). If our morality concludes that exterminating existential threats to a species has a particular moral value, then that value should apply consistently.
Here are some mind flayers. They eat humanoid brains.
Over here are some perfectly unobjectionable humanoids. Maybe they're even children.
If you don't act to prevent it, the mind flayers will eat some of those humanoids, i.e., commit murder. Stopping that from happening is objectively good.
Your means of stopping it doesn't necessarily have to be killing them - if you're a powerful enough mage or mages to put the mind flayers in an enchanted eternal sleep, or turn them to stone, or True Polymorph them and make it permanent and keep them as tchotchkes on the shelf or make them humans or rabbits or something, that's fine - but for most PCs faced with this situation, the means of stopping the mind flayers from committing murder, mass murder over time, is going to be to kill them with the means at hand. True, you could subdue them nonlethally, but even if you have the means to hold them without their powers allowing for a very real risk of escape, that may just be condemning them to a slow death as they starve, so not really doing them any favors - again, unless you have access to powerful magics which allow for rendering them not a threat on a permanent or at least an until dispelled basis.
And whatever means you choose to use to prevent them from eating people's brains, it should be either permanent or close to it, otherwise you're just delaying the problem of mind flayer defense and perhaps shifting it over to another realm that they'll find an easier skull to crack - which means the problem may compound itself as they successfully reproduce by turning humanoid bodies into more mind flayers.