Having finished the game, I don't find the Fireflies to be bad guys, especially Marlene.
I can see it being wrong wanting to sacrifice a person in the name of a cause, even an humanitarian cause, without the person's willing consent but Marlene, from her scenes, and her diaries, seemed genuinely troubled with the sacrifices she had to endure in the past, her responsibilities and decisions, and with the need to sacrifice Ellie. She didn't come off to me as a deranged person or a cold killer, but as a person who genuinely strived for what she felt best, even if she felt exhausted and had to break promises.
There is also a recording of one of the doctors, talking about all the people sacrificed till then, and the fact that they were on the verge of a great discovery concerning knowledge of the Cordyceps. The people sacrificed don't necessarily consist only of the people infected and studied, or with their bodies sacrificed for the sake of the cure, but also all the personel killed, including Ellie's mother, Annah. Fireflies seemed that had suffered heavy losses, with all the outposts abandoned, and the lack of manpower at the hospital.
And the Fireflies opposed the army because, the army forces had deposed the democratically elected government. The group demanded the return of all the branches of government, basically democracy.
Personally I can't see them as deranged sickos who just want to murder a child because of reasons.
They wanted to treat the Cordyceps condition, and wanted to sacrifice Ellie because of it.
Truthfully how many people were sacrificed in the real world, in the name of science and humanity, so that vacines and cures would be found?
Still they seem like as much as a "decent" organization as one would find in a similar apocalypse.
Observation: This thread is not to discuss if Joel did right doing what he did. There is a thread for that: http://www.giantbomb.com/the-last-of-us/3030-36989/forums/just-beat-the-game-wanna-talk-about-it-spoilers-1441232/?page=1
It is just to discuss the Fireflies organization.
I, also, may be wrong in some of my statements in respect to the contents of the diaries, because I chose to play the game, first, translated and dubbed in portuguese. So there is no harm in pointing out innacuracies.