From what I've gathered so far based on details surrounding the film along with Ledger's reported influences behind his Joker portrayal, methinks Gordon could be in for one hell of a 'dark' ride.
Here's why:
1) Ledger himself cited The Killing Joke among the works he drew inspiration from in crafting his vision of The Joker. Fans of the TKJ can clearly remember how Gordon is nearly pushed over the edge here through the machinations of Joker.
2) Gordon is no stranger to the loss of a loved one at the hands of a crazed murderer (i.e., Joker). Let's not forget Sarah Essen-Gordon.
3) In the 7 minute prologue to TDK, reports indicate that a wide-eyed Gordon is seen swinging an axe and ultimately crashing it down on the bat-signal. What could this mean? Resentment toward Batman for helping spawn The Joker and others of his ilk? Mind control of sorts? Who knows? There's a definite story there. Somewhere.
I'm sure I might have left out a reason or two to support my reasoning, but what has been stated above should be more than enough to get you thinking about the probability of Gordon and/or his loved ones being victimized for the sole purpose of driving the former mad.
Of course, it's unlikely that Sarah Essen will be introduced in the film as Gordon's mistress which leads me to believe that Gordon's current wife (portrayed in TDK by Melinda McGraw) just might be a potential target.
Any thoughts?