Not saying they intended this or are going this way, just pointing it out:
Whos city is it to lose that is also in a postion of power?
Who may not like the Mob helping the League orchestrate the destruction?
Who may be paranoid the League infiltrated all levels and may still be there?
Who promoted an uncorrupt cop in league with Batman?
Who may have a plan and resources to give Joker to hoble Mob?
Who benefits keeping Batman around to stop threats to the city such as league?
Who would have been in place or had people in place to ge to comissioner&judge?
Who is mayor and never had real name revealed?
Who is always dressed real nice, has funny eyes and uses a pen rather than umbrella?
It's a stretch, and is not cannon, but could be a reinvent for the times. Yes, I know Nolan said no tot he character. Interesting though.