Well...she regained her past. She really is no longer a puppet and she's a strong person. I bet she finds some way to live even if she naturally wields that scar for her whiole life. Or maybe she tries to destroy inferno...who knows. Actually as you said it's not even sure she survives the next 5 minutes.
the ground where the bullet casing lied looked different than where Elen were. Not to mention we saw no indication of "bulletmark" on her. Like blood and else. She's motionless, but maybe because she's so mesmerised by the sky. Anyways if they really wanted a happy-looking sad ending they should've added to casings lying next to each other. Showing that both are died. I guess they killed only Reiji because of McGuire's orders. As I said I only understand 30-40% of the conversations.
I think that Elen is also dead. When Reiji collapsed, he wasn't near Elen, he left alone for a while before that. Elen turns and smiles at the screen while vanishing slowly and then we see her lying motionless. That bullet shell is also close to where Elen is.
Still, the Road of the Cerulean Sky ending was much better in VN. It was much more action oriented and when Scythe died, he had the face as if he got bitchslapped hard. Here, he is just so happy >_>
What do you think of Elen's case? Do you think that she's dead too?