I think this is one of the themes of the SCP Foundation. The Foundation goes to enormous lengths not to kill anything unique when they can understand it. They'll even let it coexist, to whatever extent gives them maximum control. But they can't reconcile this moral conflict. They lock their creatures up to try to defend the world from them, but they'll condone spending however much of the expendable they have to in the process. And they don't really approach understanding either, because the whole idea of preserving normalcy is about protecting their understanding from what it doesn't already contain, the concept that learning about things outside of your framework of reality is fundamentally distressing and only a few special people should have to shoulder that burden.
It traps them in the paradox. They can't bring themselves to destroy the chance at knowledge, or to cleanse what is exceptional. But they still feel threatened by it, by the circumstances of the meeting. So they try to change those circumstances to the circumstance of containment, which is necessarily costly in blood, in resources, and in impact.
This is further complicated by the fact that there are often good reasons to contain something that is legitimately dangerous beyond just being weird, and good reasons not to destroy an ill-understood anomaly. These categories often overlap, creating cases that justify, even necessitate the Foundation's strategy. But necessary evil isn't generalizable beyond states of actual crisis. The classification of the anomalous employed by the 05 council treats many SCP objects as if they fit this overlap even when they clearly don't.
The ethos of "we die in the dark so they can live in the light" also describes not just the idea that the knowledge represented by the anomalous is dangerous and should be restricted, but, in my opinion, also a desire to spare the rest of humanity this dilemma. SCP Foundation employees know that even the most innocuous anomalies are threatening to the average person's sense of normalcy, and that rejecting something with good qualities for unbalancing you creates a sense of moral conflict. The dark that they die in is moral uncertainty, while protecting the light of the status quo.
It mirrors trends like color blind racism and don't say gay. The system identifies something as threatening and proscribes violence against it, then protects the conscience of the average citizen by obscuring the existence and humanity of those marginalized by this violence. In many versions of the canon, the SCP Foundation couldn't exist without the contributions of clandestine free ports like Three Portlands and Esterberg -- settlements forced to be clandestine by the policy of the veil. The status quo doesn't function without the victims it refuses to acknowledge.
OP's original observations reflect a cultural attitude of the seperation of man and nature. In particular, the exaltation of man above nature, at leisure to impose his will on it thanks to his rationality, and therefore non-culpable for destroying it when it gets in his way. It construes elements foreign to our social systems as obstacles to overcome, the only alternative being providing some use to our species. An alien, here, fills the same role as a tiger or native tribe in 19th century adventure stories -- excitingly foreign and in need of subjugation.
The SCP Foundation, appropriately, also traces its roots to the 19th century. Canons disagree, but it clearly came about at the height of colonialism, and from the merger of secret organizations largely associated with colonialist institutions, such as the British, French, and American governments, Meiji Japan, and the East India Company. The fact that the 05 council leadership has access to the Fountain of Youth has kept the core of this organization largely consistent since it's founding, depending on canon.
From those roots in determining "normalcy" in a colonialist, euro-centric context based on Enlightenment ideas of reason and science at the time, the Foundation permeated the modern world order, founding front companies in every economic sector and entering symbiotic (though rocky) relationships with nation states. In short, the Foundation inextricably became one with of the status quo they defend.
This inherent bias made the idea of the anomalous fraught from the beginning. Many things contained by the Foundation had been an accepted part of society for thousands of years, such as thaumaturgic rituals and ghosts. These were rejected from normalcy not because they were more dangerous than things left uncontained, but because they conflicted with the supremacy of the "rationalist" viewpoint.
Every alien predator, slumbering monster, even vengeful ghost has its place within the natural -- if they were truly supernatural, they would not be in nature. The horror they cause is from their displacement, their disruption, and the threat of their intersection with humanity. Many stories even emphasize the age of the creature, being from a land "time forgot" -- one that has failed to make one for anthropic progress.
Killing these things restores safety, but it also restores sanity, and the sense of living in a human made world. That is what Lovecraft often tries to convey in his horror -- that the terror of a creature may not be in what it is, but what it means for the scope of one's existence. Killing the alien is the rejection of the foreign, the ancient thing a resubjugation of the Earth. It comforts us that such things cannot challenge our place in the world. That is why Cthulhu cannot die, because that comfort cannot be restored, anymore than we can unlearn of our mortality.
Taken in aggregate, again and again, the truth of these incursions cannot be denied. The SCP Foundation cannot escape its fascination with this truth, which is why it studies the anomalous. Nor can it escape that its normalcy relies on the exploitation of what was never actually paranormal, but merely normal, and so it contains what it cannot dispose of. But the threat to the brittle rules of convention that the Foundation clings to as a essential is inherent in these beings. That is why they must be othered, for self protection.
Sauelsuesor Sedira Phoibe Ohirume-no-muchi-no-kami Galatia Nira Servus Tenebris Lucy SCP-179 put it well when she indicted the Foundation for its solipsistic priorities. She wouldn't pledge herself to them because they didn't care for others she cared for, "others beyond the little walls of rules and bone and laws and flesh you build around yourselves until you don't even remember them."
That is why we fail to see the tragedy in killing what is alien to us. Because we don't even remember that we could see it as a tragedy.
