That the fireflies may have had an ulterior motive for killing Ellie? This is a new idea of mine, so this theory of mind could have a flaw that I overlooked, but I throw it out there and see what you people think. Consider this, the Fireflies are fighting the Military and are losing. I theorize that Marlene and the Fireflies consider finding a vaccine for the infection there best chance (or hell there only chance) at changing the tide and making the Fireflies strong enough again to beat the Military. Having the vaccine would give the Fireflies a lot of power, maybe enough to overthrow the Military but I think that they would want to stay in power after they got it. The best way the could do that is to be the only group with the vaccine. So that means that they'll have to keep Ellie a secret and make sure no one finds out that they got what they needed for the vaccine from her. But that would be hard to do, they couldn't just let her go afterwards in case anyone finds out, goes after her and makes a vaccine themselves.
So what do they do? They say that they have to kill her in order to get what the need from her of course. It would be easier to defend some information and whatever then a living person. And the only way they could kill her and not be viewed as evil or whatever is if they say they had to kill her to be able to make a vaccine. I don't ever remember if the Fireflies even attempted to find anyother way to get what they need from Ellie without killing her. I can see Marlene doing something like this, I mean she's coldhearted enought to just go ahead and kill her good friend (Ellie's mom) daughter without her consent for this vaccine. And even though Marlene raised Ellie (found this out in the letter in Ellie's backpack from her mother, kind of seem like Anna died soon after Ellie was born and that she wrote that see was trusting Marlene to raise Ellie) since she was very little, she never from a strong Motherly bond with Ellie and I don't think Ellie though much of Marlene. Ellie said that Marlene was " just a friend" and when arguing with Joel after she ran away from Tommy's place she said everyone she cared about either died or left her, so she feels that Marlene abandoned her. What does that tell you about Marlene?
This is just a thought of mine and I could be totally wrong in some of my thoughts her, but again I just thought that I'd put it out there and see what people think.