The Brotherhood are presented as they are to insure that there are reasons to side against them, as any of the other three factions. As one of the most prominent faces of the franchise, which faction do you think most players would gravitate towards if they were presented as shining knights with no flaws? They probably still do, but in lesser numbers.
The Brotherhood are flawed. They have some deep seeded prejudices that they really, really need to get over. They also have a very paternalistic (and often condescending) attitude of 'we know better than any of you how to handle this technology'. In regards to the technology of the Institute, they're in the right. The Institute has committed multiple crimes against humanity with their technology, and Synths do represent a clear and present danger to Homo Sapiens as they are already being used to replace members of the civilian population.
It's not a matter of 'if' the Institute loses control of Gen3 synths (or synths in general). Or even when. They already have, and don't realize it. There are multiple synths still within the Institute organizing an escape. The Railroad wouldn't exist without the inability of the creators to control the created. Ignoring the 'are they sentient?' debate and just stating -- one way or the other, the Institute's grasp on their own slaves has already slipped, and it's the player who determines how bad it gets.
The Brotherhood's zealotry and fanaticism is meant to be offputting, and it very much is so at times. It's like that in the other games as well. They're hardasses because they think they're right. Similar to their opposites in the Railroad and the Institute. Both other organizations justify their failures (Gabriel turning raider) and their crimes (FEV experimentation) in the light of 'they are doing what needs to be done and what is right' -- nevermind those eggs that got cracked for that omelette.
On the other hand, the examples that get used against the Brotherhood the most -- Danse's fate and Teagan's moral ambivalence -- are nowhere near as negative as is frequently portrayed.
Danse is confirmed, through irrefutable DNA evidence, to be a Synth. The Brotherhood has no way to know when that happened, what Danse's true purpose is, or if he's a mind wiped Railroad refugee and essentially safe. Maxson absolutely makes the right call to have him executed as a potential threat. For all he knows Danse is either a spy (and all their plans are compromised) or a saboteur that will try to destroy the Prydwen or an assassin that will shoot him or his senior staff the next time they see each other. Danse even admits how much worse he made it all by going AWOL instead of facing the music -- and he did. That was the absolute wrong move on his part. That Maxson is able to be talked down to commuting the death sentence to exile shows that even in the heat of the moment he can listen to reason.
As a player, I like Danse a ton, but even I can see that Maxson wasn't wrong here. He presents the command like any military commander would -- you will do this because it is my order -- but even when faced with insubordination and highly emotional himself over feeling betrayed, he does listen to what's being said. Danse can be spared and be allowed to live without being specifically hunted down (just subject to attack if crossing paths with a patrol or entering a BoS facility).
Teagan, though, is definitely a grey area. Lancer-Captain Kells, the second in command of the expedition, explicitly states that the Brotherhood is on orders to be on their best behavior to make a better impression on the Commonwealth. That they expend so much material and manpower on putting down threats to civilians with their vertibird patrols shows just how dedicated they are to that directive. Teagan, likely, is being borderline insubordinate himself by making his life easier by letting those working for him use 'whatever means necessary' to reduce his workload and make sure the supplies are brought in. At the same time, his toleration of immoral methods of procuring crops doesn't force the player to do it that way, as there is both the option to convince the farmers it's the right thing to do or simply to pay them a fair price for the crops.
To give you an idea of what the prototypical BoS member thinks about the quest is the fact that the only outcome in the quest that will get a 'Liked That' response from Danse is paying the full purchase price without haggling it down. That's likely the first choice of most knights, considering how much Danse models the 'ideal' prior to Blind Betrayal. Haggling, Convincing, or Threats are neutral. Murder, of course, is not ok with Danse. As tolerant as Teagan is of the various tactics for this quest, though, it's the Survivor who chooses how it ends, and that responsibility lies on them, not Teagan.
The real debate, I think, is over the quest Tactical Thinking and the order Kells gives to take down the leadership of the Railroad. With the desire to destroy as many Gen3 synths as possible when the Institute is destroyed (by insuring they never escape), the Brotherhood performs what is their most questionable act while in the Commonwealth. There is no way to influence the quest like with Feeding the Troops. Here, once the quest is accepted and the Old North Church entered, it can only end with the death of Desdemona and the entire leadership of the Railroad. There's no way to warn them, or to spare them. They will already be hostile to the player before they even leave the Prydwen.
As a person, I feel it was excessive. At the same time, I can see the Railroad was a threat, as they certainly have the ability to plant a bomb on the Prydwen as shown in Rocket's Red Glare. It's about whether they survive the raid on the Old North Church HQ -- and if the player sides with the Brotherhood, that is not a possibility. Also, if you do not view the Gen3s as 'people', then it does make sense to insure they're all in the biggest group possible for ease of destruction, even if it's done in a very heavy handed way.