Just because you choose scummier individuals to perform experiments on doesn't make it any more moral and ethical to do than if you did it to a toddler. Just because the collateral damage is more 'acceptable', it doesn't absolve you of crimes against humanity.
Disliking Roger Warwick's alcoholism and abuse doesn't mean he deserves to die. He deserves punishment -- whether that be removal from his home, time imprisoned, or some sort of frontier justice like a savage beating -- but it's not a capital crime that he's guilty of and there's no justice in what happens to him. If he'd been a saint, the Institute still would have killed him and replaced him. They did it because he lives in a sanitation runoff area.
That also puts the question to -- what did Mayor McDonough do to warrant being replaced and murdered? Because we have no idea when it happened, it is very possible it was the Synth that had the ghouls thrown out of Diamond City, as Hancock says his brother was not the man he recognized anymore by that point. And the countless others?
As for your question about Supermutants, according to the Wiki:
"While they will not normally die due to the normal effects of aging, super mutants are prone to senility, leading to tendencies to engage in near-psychotic, aggressive attacks against other humans and other creatures."
"Fawkes also reveals that the "super-mutation" causes extreme pain and that it's the key factor that turns super mutants feral and inhumane. Fawkes states that he barely withstood it himself."
Not all are complete rage monsters, but the vast majority are. They are in agonizing pain constantly, and their heightened aggressor hormone production keys off this. As they get older, they get dumber, and are less and less able to fight the constant pain that causes the rage. I can count on one hand the number of ... reasonable... supermutants that have been shown in the various FO games.
You'll note even Virgil, a fairly calm and sedate scientist, is slurring his words and losing his fine motor control already.
This is just a bad argument. Why should you not just walk up to everyone you meet on the street and blow them away with a shotgun? You don't know they're not a bad person!
Murder is murder is murder. Outside of self defense (which is what killing Raiders or Gunners is), defense of others, or within the boundaries of warfare (combat between the factions - and there are plenty of people in the modern world who think even this is), murder remains murder, even in the wasteland.
Killing the real Art for any reason after the dialog choices is a murder, plain and simple.
Warwick's death is murder. All the dead supermutants in the FEV lab are people that were kidnapped, experimented on, and then murdered.
Every person that is killed by a supermutant the Institute released (or someone turned into a supermutant by the supermutants released by the Institute) is someone that was murdered, and the Institute is ultimately responsible for it.
The Institute is a damn murder factory. It's one of the many reasons I dislike the faction so thoroughly.