Also, I think her willingness to go against the whole city was more an emotional decision made in the heat of the situation rather than a logical one. In other words, Mikoto had snapped a bit here (I recall one scene where she descends a bit into "mentally cracked laughter", which is one reason why she reminded me of Sayaka). Mikoto hadn't snapped to the point of no return, but she had snapped to the point where she was willing to do truly insane things to stop the slaughtering of her sisters, and she truly needed Touma to bring her back from the brink.
Once Touma managed to get through to her, and help resolve the most pressing problem, Mikoto sort of snapped
back into more logical lines of thinking, and basically just dismissed her earlier madness over going against the entire city.
And yeah, I agree with Qilin about Mikoto being Neutral Good. She's not Superman; she doesn't hold herself to lofty ideals and firm concepts of justice. She just stands up to evil where she happens to come across it. If Mikoto cared
that much about justice, she'd probably be in Judgement, and she probably wouldn't be picking fights with Touma so much.
