I think Gordon actually ends up in the hospital after Bane takes control. Remember Gordon's lines in the teaser "We were in this together, and then you were gone" I think Gordon is referring to Batman's disappearance after he gets beaten by Bane and exiled to the underground prison. Only Bane and his men (and Catwoman) will know that Batman has been beaten and captured. Gordon will think Batman dead, or may have fled after his recent comeback, he has no way of knowing that Batman is beaten and now a prisoner. And I'd venture to say that scene with Gordon and Bruce in the hospital occurs as soon as Bruce returns to Gotham from the prison. He is obviously not wearing his cowl in the hospital based on the dialogue, I imagine he is wearing a ski mask to bring things full circle with Batman Begins. In Begins his first encounter with Gordon after returning to Gotham was in a ski mask in Gordon's office, and now he dawns the ski mask again meeting Gordon in the hospital. Not to mention he probably needs to craft a new cowl after Bane breaks his other one, so him wearing a ski mask makes sense imo.