It can be incredibly difficult to stand up for your siblings, especially as a girl raised in a Mormon household. I say it that way, because Mormon culture places the woman beneath the man. Not to the point that she's property or something as backwater as that, but to the point where in a contest of authority in the household, the wife is always expected to bow to the husband's perspective.
It's a terrible, horrendous, system, but it also explains why Emma would have a hard time standing up and decrying her parents' actions publicly, but would seek to love Ian and Silas in secret.