The way I see it, Nolan has conciously (or sub conciously) put his politics into the movie.  Lets have a look.

Batman = Idealized America
Joker = Terrorism
Dent = Iraq

In the end Nolan is saying that although America is trying it can't defeat Terrorism without destroying Iraq.  And when it does it will have to accept the cost.  A world that hates it and has to chase it.  In spite of it's good intentions.

Now let's look at some thing to support that theory.

Batman = Idealized America proof:
1. Batman has to do what is right, not what's popular.
2. The citizens turn on Batman when too many of them are killed.
3. Batman poses over a falling building like 9/11.
4. Batman carries out operations overseas without going through channels.
5. Batman violates privacy for security with the sonar (patriot act)
6. People copy Batman but don't respect him.

Joker proof:
1. He's called a terrorist.
2. He uses suicide bombers
3. He talks about killing those with a plan (those in charge)
4. He uses and burns oil
5. "look what I did with a few guns and some gasoline."
6. He makes videos.
7. He tries to recuit people to his cause.

Dent proof:
1. He's fought over by Batman and Joker
2. He is hurt because of oil
3. He loses an innocent life (Iraqi civillian)
4. His way of thinking is overthrown with another.
5. He doesn't trust Gordon but works with him. (I'm working on the Gordon = Military theory)
6. The longer the fight the more unstable he gets.

Now.  Look at some of the situations.
Joker and Batman are compared constantly.  Not just said out loud by Joker but they have similar actions (Asking about Dent, not drinking their drinks, immovable objects).  And the Joker gives the dark prediction that the war won't end "We should do this forever".

There is a moral experiment at the end.  The americans on one boat and Dent's guys (Iraqi civillians) on the other.  They are both shown to be equal in respecting life.  Being Iraqi doesn't mean you are a terrorist.

Gordon holds everyone in his holding area instead of putting them in county lock up.  Could this be the military taking people to Guantanamo?  Dent was against it.

Gordon says he saved Batman, just like the Military has been protecting America.