Synths being intelligent is a whole separate (and extremely long) argument.
For sake of brevity I'll state two considerations. One if they are, one if they're not.
If they're not sentient, the BoS are not responsible for anything more than destruction of private properly when it comes to destroying them. Hardly a heinous offense. If they are sentient, the BoS is guilty of any crime they commit against them that can be shown or proven from canon (in game typically) information.
That largely consists of the large number of them that die when the Railroad and later the Institute are destroyed if the BoS are the faction chosen by the Survivor. This is a faction that hates synths so much they allow Curie and Nick on their capital ship, and while Danse makes some snide 'donate yourself to science' comments to Curie, being snide isn't a crime. They're never shown (and none of the radiant quests have you try) going house to house, proving who is a synth and who isn't. They take down groups of Gen1s and 2s that escaped the Institute (neither of which are sentient beings), as Maxson says they will, but that's as far as you see them go.
As for University Point, you really need to go back and read all the notes and emails on the terminals. In 2285, a young girl named Jacqueline Spencer found data on an old system (since she's a tinker in her spare time) belonging to the University faculty before the war. In it there's a rumored research facility somewhere underneath the University. Jacqie can't figure out where as most of the rest of the data is corrupted, but she keeps looking. Her father is a merchant and the next time they're in Diamond City she asks around to see what something like this is worth. The rumor makes it back to the Institute, who sends Kellogg. Kellogg gets there, immediately approaches the mayor and tells him to hand over the research data (even though they don't really know what it is yet) to him in two days or there would be major consequences for the whole town (which is one of the three largest cities in the Commonwealth... this isn't some hamlet, it's dozens of citizens and families).
The threat is on a holotope voice recording, so it's very, very clear what is up and who it is. The town immediately goes into an uproar and multiple residents start threatening the young (and now very scared) young woman. She desperately tries to find the data of where this facility is located before Kellogg returns.
She's not fast enough. She finds the information on a terminal as everyone in town is being gunned down by synths and Kellogg at the Institute's orders and re-encrypts the terminal before Kellogg kills her, too (which he does). The item being researched? A new type of laser rifle that had the 'Neverending' legendary trait. The synths are still there at the beginning of the game, searching for what they cannot find.
This was in 2285, under Father's Directorship. There is no mitigating circumstance where any of these acts are acceptable.
Supermutants and the FEV -
It is absolutely certain that Father monitored and directed the research. Virgil's recordings are very clear that it's Father he's asking to shut the program down and who keeps refusing. Zimmer and Syverson were just as important to the program as well. Clayton Holdren obviously knew about it and is HEAD OF THE BIOSCIENCE DIVISION predating Virgil's flight to the Glowing Sea. There is no way this man was not a part of a project that had a whole wing of his Divison sectioned off and dedicated to it. That he was head of the Division meant he also had other projects to work on, which is why Virgil was head of the FEV program. Just like Karlen is in charge of the gorillas.
Justin Ayo and Alana Secord absolutely knew about it as 1) they're in charge of what is basically the security apparatus, so would know and would be responsible for policing it, and 2) because they were the two in charge of the division that secured the specimens for the research as they administered the Coursers and the Synth security patrols.
I have no doubt that people like Li, Fillmore, and others like Binet had no clue about the FEV. Li herself immediately leaves the Institute if you hand her the tape of Virgil's you find in the FEV lab.
Roger Warwick -
Warwick was a mess of a man. A drunk, a wifebeater.
The world doesn't actually miss him. Thing is, killing him as they did is still murder. Just like walking up to a drug dealer and suddenly stabbing him in the neck is, too. Sure, no one will miss his passing, but you're still going to prison.
And yes, he was taken by the Institute. It specifically states under the Warwick Program notes on the Bioscience terminal that Warwick was 'acquired' and 'interrogated' so that they could program his Synth replacement. The only kidnap victims that leave the Institute alive are supermutants when they're released -- they are essentially dead as the supermutant has no memory of their old life previously (typically, there are rare exceptions), is a psychotic rage monster, and viciously homicidal.
That still doesn't explain McDonough, who was blatantly replaced for political reasons. He was a real person beforehand. He has a confirmed brother in game (Hancock), who describes no longer recognizing the person he grew up with by the time McDonough was elected.
As a noteworthy comment -- No matter how much you may dislike the BoS and RR, there is an option that isn't even possibly 'just as bad' (and I still strongly deny that any of the other factions come close to the level of 'bad' that the Institute is) as the Institute. The Minutemen present a clear choice of a morally upright faction that is honestly trying to do the best they can. Yes, their old leadership collapsed and they lost a lot of men to becoming gunners, raiders, and mercenaries.
That was those men quitting the organization, and then becoming worse for it. Those that remained (or came back) are the most loyal of the bunch, and in rebuilding the Minutemen you have a group that protects the common man, helps make sure they are fed and secured, and treats synth and human alike the same, as long as they're willing to work hard.
It's the faction that is built the way you, the player want it, and if you want them to be the good guys, then by god, they are. They're not flashy, or glamorous, or fancy, or high tech. They do bust their butts working those fields all day every day, and answer the call even when on a 1 to 1 basis they don't stand up to anyone else's fighters. Most to lose, least to gain, and they still charge into the Institute with you.
But because Preston Garvey's radiant quests are annoying, half the time, most folks wouldn't consider them.
Even already in my playthrough, there are Minuteman patrols everywhere because I took the time to build up every town. I see them on bridges, securing buildings, fighting off Supermutants and gunners and raiders constantly. With maybe some leather armor and a laser musket. They're the dang heroes of this story.