I think the stories continue to be better written this season than any of the previous ones. It did give us a lot of backstory on Haley--enough to know she is more of a purist than thought. And gave us J'onn's future work too.
However, the last scene made the episode for me. In terms of acting and shock value.. it was so unexpected. Also, they have with that one scene raised the stakes.
I am not sure whether the Alex thing is a good thing or a bad thing. What if they plan to make her the season or series villain based on this? That'd be honestly my worst case scenario for the show.
However, if written well and if it ties well into the rest of the arcs--somehow leading to some breakthrough for Kara/Alex or both in CoTL, Manchester Black or the President thing--then, it could be a great story.
In context, I thought it made sense that Kara said that about becoming Supergirl. At least, that is how our minds work--It's true that Kara is a hero who would help everyone no matter their importance to her; but it is also true that at the time, Kara risked her identity for Alex's sake; and may be that is what came to her mind when the talk was of Alex forgetting all about her (who Kara is.. it is not just about Kara being SG after all, it is about her being alien, superpowers and almost half their life together).
Kara losing the key element in her support system is not good.