It's not a red flag if they've already distanced themself from you once and then during that period, you were permanently disfigured. It is, in fact, a perfectly reasonable reaction.
She's not making passive-aggressive or manipulative comments for attention; she just wants to go off on her own and be sad.
All the joking aside, It feels like the story is actually progressing a bit more lately. Before that it was pretty stagnant and focusing more on comedy for quite a while. Really looking forward to how it goes from here.