I dont think Marlene knew just how close Joel was with Ellie.
Let me just say, I'm still mostly on the fence as I think there's evidence that she did know. It's also a very human thing to assume 2 people traveling together for months will bond and get close, especially an orphan child.
I saw a lot of people yesterday refer to this line from Marlenes recorded message to Anna "I'm not about to kill the one man in this facility that might understand the weight of this choice." as evidence that Marlene knew Joel wasn't going to accept Ellies surgery/death because how close they are.
Full recording goes:
>Hey Anna... It's been awhile since we spoke. I uh... I just gave the go ahead to proceed with the surgery. I really doubt I had much of a choice, asking me was more of a formality. I need you to know that I've kept my promise all these years... despite everything that I was in charge of, I looked after her. I would've done anything for her, and at times...Here's a chance to save us... all of us. This is what we were after... what you were after. They asked me to kill the smuggler. I'm not about to kill the one man in this facility that might understand the weight of this choice. Maybe he can forgive me. Oh, I miss you, Anna. Your daughter will be with you soon.
I interpreted the recording as mostly about how much it pains Marlene herself to let Ellie go through the surgery. She knew her from birth, was close with her and her mom, and she would've been the one to escort her had she not been hurt at the start. If and I mean IF Marlene knows about Joels situation with losing his Sarah, I think THAT may be what she's referring to. I dont think she means "Joel understands because he doesnt want to lose Ellie either", I think she means Joel understands the pain of losing a daughter, which Ellie was to Marlene, in a way.
As for why she hopes for his forgiveness, it doesn't necessarily mean she's sorry for taking Ellie from him, but she hopes he wont judge her too hard on this sacrifice that she (Marlene) is also making. He had his daughter taken from him unwillingly, and she has Ellie alive and well but is willingly allowing her death. Or better yet, forced.
At the end of the day, the whole situation is just messed up. It could be a little of both, or I could be totally off the mark. I'm someone who understands what Joel did to save Ellie but I'm not someone who thinks the Fireflies and Marlene are evil and deserved what they got. Just throwing my 2 cents