The Institute has long ago breached the most basic codes of ethics that have stood the test of time in science and medicine: first, do no harm. But their biggest foible of all? The one that reveals both their malice, their arrogance and their complete disregard for ethics, human well-being and logical coherence?
The make organic entities, that have been painstakingly engineered to pass as humans, they apparently "teach" these entities to behave as if they are humans, they kidnap real people who have committed no wrong against them or anyone else, and then they assign these "synths" to impersonate those people, all the while stating "Synths are not humans."
Let us stop and consider the full meaning of that statement "Synths are not humans." I agree with it, but what does it mean? It means that a human being is the height of moral and ethical imperative; despite its gross perversion from acceptable standards, the Institute by using this phrase repeatedly acknowledges that human life is the "pinnacle" of moral and ethical standards. At the same time, they treat human life as it was as inconsequential as a lab rat, and then to add cruelty and malice to it, they infiltrate human communities with their synths which they acknowledge are NOT human.
If they are not human, then why do you fricking DESIGN and PROGRAM them to mimick humans!?
The Institute is as bad as the worst genocidal social organizations to have ever been known in real history, if not worse.
It does make sense that a desperate group of scientists, locked underground in a post-apocalyptic world could veer this far down this cultural evolutionary path of pure evil, but there has assuredly been naysayers along the way and we see what happens to them. It is an authoritarian and inherently "anti-human" organization and there is not suitable end to it except for it to be dismantled and everyone involved to be held accountable, ideally by tribunal but short of that, by bullet to the head if it is the only expedient solution. I would even go so far as to agree with the Brotherhood that their technological knowledge should also be destroyed because it is so inherently perverted into evil--at least in the moral vacuum of the post-apocalyptic Fallout world.
In the real world, we can handle these things that push our ethical and moral standards, but in a post-apocalyptic world devoid of social order, jurisprudence or free press, it may well be that an "authoritarian" organization like the Brotherhood is a necessary evil. The Brotherhood is loathsome too, but orders of magnitude less so than the Institute.