There's probably no need for your daughter to "make peace" with Si, but perhaps she could try on the idea that sometimes three-parent set-ups might work for *other* people. This way she doesn't have to change her own preferences for herself, but she can still be tolerant of other people's life choices. One thing that might help is for her to realize that the set-up with Si wasn't done the best way -- most importantly, that there wasn't consent all around (Matt didn't consent to the arrangement, even if he didn't put up a fight at first). Of course there is also the factor that it looks like Si wanted to "take over" eventually, perhaps even scoot Matt out of the picture.
Ultimately, your daughter will have to come to her own conclusions about what the people around her say.
Love means never having to say, "Put down that meat cleaver!"