One of the BIG revelations in the FO series is that Vault-Tec betrayed pretty much ALL of the people that sought shelter in the Vaults. Just one HUGE human behavior experiment, using hundreds of thousands of people as involuntary guinea pigs. The normal knee-jerk reaction is essentially, "That's utterly reprehensible!" [Any certifiable sociopaths or psychopaths can leave this thread now. That would be anybody that disagrees with the previous statement.]
How is the Institute any better than Vault-Tec, morally speaking? If anything, the Institute has destroyed more human lives than Vault-Tec over the last couple of centuries. Directly, in their experiments and manipulations, or tangentially by sending killer synth squads to eliminate any inconvenient humans that posed a threat to the Institutes machinations. Guinea pigs or cockroaches, the Institute seems to be thoroughly uncaring that it has been human beings it was destroying.