Why is the rape scene important?
...with the incident, it became less clear whether the parents were at fault (i.e., for disallowing their relationship) or the children were at fault (i.e., for failing to believe their parents) ...

I thought that the dual nature of the relationship was established prior to that. Qinghong's suffering was internalized early on, and I think Wang should've left it as such. 

-- More importantly, I thought it was also symbolic of the "migrants" who were "raped" of their dreams (like the children's) ...

That's rather heavy-handed "symbolism" don't you think? Perhaps something that wouldn't look out of place in a TV Drama.

-- But, if she cried because her parents have insisted on charging the guy (and eventually caused his execution and death), then she probably still loved him ...

Are you sure that he was given the death penalty? I thought his name was one which received the life sentence.