Except the part when they are responsible for every single mutant in the Commonwealth. Because they released them for fun or something apparently. They must have dipped thousands of wastelanders in the process, just to kick back and watch the fireworks of mutants eating people alive.
The Institute is cartoonishly evil. There's no moral ambiguity when it comes to them. Initially you can be tricked into thinking they are, but only for the first playthrough. But once you know the full story, you realize that Elder Maxson has a point when he says they are a cancer. There's no debate, there's no question about it. Cartoonishly evil to the core.
You can say "Well I can change them myself as Director." But no, you can't really, because there's nothing you can do in-game to actually change Institute policies. Nothing. Which gives the only possible reasoning for siding with them as a good karma character a swift kick in the ass.
The only moral ambiguity when it comes to Fallout 4 is "Do I think Synths and ghouls deserve to be exterminated?"
If your answer is yes, welcome to the Brotherhood.
If your answer is no, then welcome to the Railroad or the Minutemen.
Them's the breaks.