People have definitely noticed the social commentary. It was pretty obvious, especially when it came to Monroe and Rosalee's wedding. :)
And yeah, while I could understand Juliette's fear of Nick (it's basically an extension of how revolted she was with herself)... they make sense from a character perspective, but not so much from an allegorical perspective.
I'm not sure I agree that the OL Wesen are persecuted... or, more accurately, they're not persecuted by the people that they're attacking. They've been attacking Kehrseite. Who, being Kehrseite, are completely unaware that there are even people who are different from themselves... so how can they be persecuting Wesen?
This is one reason I initially thought (before the season started) that the uprising would be against the Wesen Council. Because, if Wesen see themselves as being persecuted, the Council is the obvious choice for persecutor - they are, after all, a small governmental organization that primarily rules through fear. But there's been like one dropped reference to the Council so far this season, and it wasn't even in the right context!
So it's kind of hard to sympathize with the OL. In fact, everything that I've seen of them so far, says, "terrorist organization" to me. There's the (somewhat justified) cause, the conviction that what they are doing is right, the willingness to commit suicide for the cause, the willingness to murder random people for the cause...