Has anyone considered the idea that perhaps Lilly doesn't leave the group of her own free will? There is the option that she gets somehow seperated, much like Andrea is seperated from Rick's group in the TV show , as has already been suggested. (I personally favour this idea)
But what if we get a more Shane-like scenario, where Lilly loses it completely and is consequently exiled. We can see clearly in the preview for episode three that Lilly begins to really lose her cool, when she shouts something along the lines of "I'm not gonna let one person fuck this up for the rest of us!" and then we hear a gunshot as the screen cuts to the title.
I'm not suggesting Lilly is shot, because Canon demands that she is to survive long enough to do what she does in Woodbury. But what if Lilly offs a member of the group in a rage? Or tries to? Wouldn't the group leave her behind for the safety of everyone, especially the children?
Of course, there are holes in this theory. For example, those who play a Lee who have consistently sided with Lilly over Kenny could rightfully argue that in this scenario, Lee may still support her reasoning for breaking down. But at the end of the day, Lee has Clem to look out for - and yes, Kenny may be an asshat - but he has the RV, and Lilly has lost her mind. Lee will do what's right for Clementine.
Blind speculation of course, but I thought I'd throw in my two cents.