Well we don't know exactly how it broke down, but needless to say The Institute must have felt terribly betrayed. Someone, somewhere must have done something stupid like try and usurp power and kill everyone else and make himself King o' Town and The Institute got caught in the crossfire.
So then they just said "[censored] it" and decided to dig-in and protect their own.
Perhaps yes. But The Institute did create them after all. Spent hours and hours tweaking their programming, dealing with buggy constructs, and working out kinks.
We just get to see the fruits of their endeavors. Like Danse, Curie etc. We don't get to see, for instance, a version of Danse who can say nothing but "I like Fancy Lad Cakes" in a very, very monotone voice or do some sort of awkward creepy robotic walk because they hadn't figured out the speech or motor functions fully yet.
For an Institute scientist, its hard to look at Synths as much more than just things they spent ALOT of time and effort building. But even Father cracks a little bit, as he does with Synth Shaun. And of course there is Dr. Binet who's a full-on "Synths are people too!" radical.
For some of the scientists, its probably anologous to an artist's painting getting up and walking away because it wants to be free instead of hang up on your wall like you intended. If you spent all that time and effort making the painting you'd probably be less inclined to grant it freedom.
Well even Codsworth and the like have the ability to "feel pain" (to use that term a bit loosely). Because they all have damage avoidance protocols. Just like ED-E in New Vegas. Whom that one Doctor (Whitley or whatever) argued was "being hurt" when they didn't disable damage avoidance during testing.
Ultimately it makes sense. You need Synths to protect themselves and not accidentally walk into a fire because they forgot fire burns.
Its kind of cruel that humans feel pain as well. But its necessary for our survival.
Well either way she sticks with the SS as a lover, so she must not feel too betrayed. Or maybe she's just lovestruck.
Either way, I guess the interpretation comes down to do you intend to follow through with what you said, or not? Prove Piper to be naive or actually commit?
Its up to the player. Ultimately.