Lily will be back for season two here's why...
In season 1 when she asks Lee if him and Clem wanted to go with her you have a decision to say yes. If you do then it will say Lily will remember that. This only happens if you agree to not leave her on the road.
Plus in season 2 you get a chance to mention Lily to Alvin. Could Lily be at the camp with the 400 day's characters or Carver's group?
Maybe you will run into Lily and depending on what you did in season 1 she will remember what you did. She will be shocked Lee isn't with her/she will talk bad on Lee if you chose to kill Larry with Kenny. Clem will be upset and question her why she killed Carly. Lily will try to explain it to her.
Maybe when the Van's gas ran out she ran into Tavia's group and helped the group.
I don't know I just think we will see her again. Lily is tough and not that stupid to get bitten by a walker. Lily is a trained military personal so she has the skills to survive. She has no beef with Clem because she was young, but now that Clem's grew up they might have beef knowing that she killed Carly/Dough.