I suppose I would submit you are the blind one if you cannot see how anyone could perform those actions. Remember that you are playing a game where you are alive because you placed your trust in a company that decided to use you as a popsicle experiment. Tack onto that the fact that there are any number of random locations showcasing how a few psychopaths can cause a gross amount of misery and death by virtue of their placement (Hallucigen comes to mind). Really, I think your fear of a synth takeover/massacre is predicated upon fear and naivete. Certainly synths could cause untold amounts of harm if they infiltrated mankind for the singular purpose of overthrowing some structure, but:
1. That purpose is pretty much nullified with the destruction of the Institute. The Institute created gen 3's for the purpose of infiltration and without them to pull the strings, synths have absolute freedom in how they choose to act, with all the risks and dangers that entails.
2. Diamond City is an anomaly in the Commonwealth, and even being a structured settlement, the power structure rests upon several individuals. In other words, you'd have to kill a lot of people before you'd destabalize anything and that would ONLY be diamond city. There are plenty of other self sufficient settlements. That's not to say that we should take risks because we can, but there is a level where you stop being reasonable and start being paranoid. You have to ask yourself what synths would stand to gain by killing humans now that they are no longer under direct control by the Institute.
3. You have direct multiple examples of synths who demonstrate they are under their own willpower and not beholden to some higher directive. Paladin Danse is the perfect example. A man so beholden to the virtues of the Brotherhood, yet when he finds out he is a synth, he STILL holds to those principles. Valentine likewise is very self aware about his status as a synth, how that makes people nervous, and how he is grateful for the chance he had to prove himself to the people of Diamond City.
So basically, the question becomes rather simple. Are you willing to condemn a group of people to death because some of them might be psychopaths? I leave you to decide.