I really would like to engage in deeper discussion about this "why isn't Academy City getting rid of Mikoto after what she has done?", but I feel that this question is approaching the level of the "Frodo Plot Hole" meme.
In short, I feel like being trolled.
And besides, a deeper explanation would require information from the light novels, which is more or less not allowed in the manga thread.
But to heck with it!
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The only reason why Mikoto and some level 5 are being left alone is because they are INSIGNIFICANT TO THE PLAN
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I disagree. She is the third most important person to the plan, that's why she's ranked third.