I agree... I was trying to forget that.
Anyways, Season One... I don't think Alex was condescending after that pilot (I have a feeling they changed some bits after it)... Not completely sure of Kara yes, because she herself was growing into her role.
I have kind of liked the non-Maggie bits we got in early S2 and whatever of the sisters we got in S3 except when they were talking about Sanvers.
Anyways.. it appears that everyone is pretty much agreed that Alex should have been worried about Kara--it'd have made most sense and pointing towards Maggie was just weird and questionable writing.
So... I will stop my argument... And really hope that if Maggie comes back even for an episode, it will be with another girlfriend in her arms... So, that Alex will never mention Maggie ever again.
Gah! As I have mentioned elsewhere, I have never disliked a character as much as I have hated Maggie since episode 11 (the cupcake episode?) of last season. The writers just write Alex weirdly to force the romance and then make Maggie out to be some great love interest while she has been one of the least trustworthy people around. Manipulative, aggressive and not respectful of the sibling relationship. Or anything or anyone Alex cares for for that matter including Winn.
I prefer Alex reasonable, and a strong support for Kara, and a kick ass Agent/scientist. Which she is most of the time when Maggie is not around.
And.. I agree with Brierrose. In fact, I see it in my head that way. That Alex was actually keeping from Kara how much her being beaten up by Reign had affected her. I am not too sure if they will actually show it though.