Sounds like dad might be forced to take his son to mom and take him for a dip in the Lazarus Pit. Or dad would probably be against that, so mom would probably handle it herself and get Damian on her side.
I like Damian and wouldn't want to see him go but sometimes the popular characters do need to die or there's no impact and less suspense.
Even though not officially, wouldn't it be fair to think that Joker may consider himself part of the Bat Family? Perhaps he means that he will make Batman kill him and go against his code? Just a thought from a newbie.
The thing that will be hard to overcome with this movie is the portrayal of Batman. How do you overcome Nolan's Batman in a brand new movie, when you haven't had time to at least flesh him out for the audience? I think as hard as it will be to make the other characters come alive for the audience(it will be harder to relate to the super-powered heroes over the less so that Marvel offers), the whole new Batman thing will be their biggest obstacle. I think they're rushing this thing and it's a mistake. I would take the Marvel route and give them their own movies first.
Being new to comics and not knowing a lot of the past relationships, I thought DC handled the relationship between Midnighter and Apollo very well in the New 52. They made it known that they were hooked up, they would have panels dedicated to it here and there, but for the most part they were just superheroes fighting crime/evil.