Synths aren't predisposed to murder; a community that could have a killer synth could have a killer anyone else.
A war that happened only because of the Brotherhood's predilection for murder, then. I also have no idea how one could call the Railroad insurgents; they're not rebelling against anyone.
So, for "the sake of argument," you're ignoring one of the most fundamental points of contention, that synth brains are insufficiently structurally or procedurally different from human brains to demonstrate that humans have free will and synths don't? That doesn't leave much of an argument.
I find this endlessly hilarious, as that was not an unquestionable opinion at the time. Many serious scientific arguments were made that black people didn't count as people. They were [censored], true, as are the arguments about gen 3 synths. Previous synth generations, on the other hand, appear to be just human-shaped robots, some of which might qualify as sapient enough to be people, but I'm not sure whether they have the programming capacity for it. Not even every Mr. Handy model has the same level of intelligence, so earlier gen synths might vary just as much.
I think that the Institute can offer a better future to the Commonwealth than the Brotherhood can, if allied with the Minutemen, for two reasons. For one thing, the Institute is much more mobile, able to summon reinforcements anywhere at anytime, and can engage in much more rapid response. Secondly, I believe the negative aspects of the Institute will be easier to fix than those of the Brotherhood, because the Institute is selfish and pragmatic where the Brotherhood is zealous and ideological. The Institute doesn't much care how things are done as long as they get done, so a Director with a strong moral compass and an equally strong ability to create solutions can tweak their path enough for things to improve. I think the Institute's most lacking trait is a sense of perspective anyway, which a Commonwealth-dwelling Director would provide.