Rat catcher has been confirmed death in the arkham comics. So I don't think its likely
I read that he might still be alive because some of the thugs mentioned him still being alive.
Arkham City Incident
The Ratcatcher does not appear in-game, although he has been mentioned as being locked up in Arkham City and hiding, in fear for his life. He figured that he could sell items that his rats found in the sewers of Gotham City, creating a small market. This attracted the Penguin's attention, and some time later, Otis Flannegan was dragged into the museum, screaming for his life, never to be seen again. Penguin's Gang mentioned that he was supposed to have ironically been eaten by his rats, but after they ignored him for several days, Penguin tossed Ratcatcher to his shark Tiny, who presumably ate him. While it is believed he is dead, a conversation in the game can be heard between two thugs discussing another thug being eaten alive by rats, alluding to the possibility that Otis was still alive
. He was also mentioned in a riddle that can be found in the Industrial District.