Can you remember the rooftop that Scarecrow pushed Barbara off? If you can find that one again, take the elevator back down and you'll end up in the Red Hood battle room, enter the floor grates near to where you discovered Gordon when he was being held captive, and head in an Eastern (I think) direction, near to where you get the option to 'Grapple up Shoot', to the right of this, you should be able to exit the grate just by walking forward (this is where you first entered the room, after the Batmobile was destroyed). I'm pretty sure that no trophies become unavailable after apprehending Scarecrow, some can just be a bitch to get to.