I think this is drastically off the mark. First off, who's let Ali off the hook? He is a self-centered monster that will happily do anything if the price is right. He indoctrinated child Setsuna and his compatriots to kill their parents and commit terrorism under the pretense that God wanted them to. His is a twisted personality whose foundation can't possibly be traced back to something so broad as gender. How could such behavior be considered "expected" based on that by anyone? I think Grenzer is basically on the mark, but I'd add that nobody would go and say "gosh, that Ali guy is actually not such a terrible villain."
Likewise, outrage at Nena has nothing to do with her supposedly breaking her gender role. It has to do with the fact that she indiscrimately murdered civilians, and moreover did so out of spite and seemingly for her own amusement. The fact that the attack comes out of nowhere and involves Louise and Saji also, yes, does add to the shock value of the whole thing.
Also, if you don't think the series has been serious up until this point, I'll have to adamantly disagree. Obviously the show is entertainment, but from day one it's been tackling various issues amiRABt all the action scenes. It's presented CB's ideology while also showing critical views of it and portraying how the Gundams' actions have affected the world. It's gone out of its way to show that Celestial Being has many good and bad elements, with the Thrones now being established as a very, very bad group. This both elevates the Gundam Meisters as heroes and yet casts the righteousness of their organization's cause in doubt. It's an impressive duality, really. You also have several subplots tying into very troubling issues, such as genetic engineering gone awry (Alleujah and Soma) and especially terrorism (Setsuna's past, Lockon losing his family, the entire Azadistan story). I mean, lord, between Azadistan and Alleujah taking out the super soldier facility, this series was supposed to be lacking in tragedy before now? Forgive me if I don't subscribe to that notion!
I think it's fair to say that issues have been raised that should be taken seriously. To reiterate, it is entertainment, but ultimately this doesn't say much. Every series has different merits and intentions, and it's on those specific terms that it should be judged.