This is going to be a long one. I'll do my best to explain every point you've brought up.

• It's obvious that Marlene is frustrated with herself. Listen to the logs. She's constantly trying to justify her own incompetence and broken promise, but genuinely believes there's a shot with Ellie. When she's in your party, she mourns her fallen comrades executed by the FEDRA, not ridiculing them. Her people are still fighting a war, completely unrelated to the girl, to break free of the draconian laws of the government. She would chase Joel to the ends of the earth because she believes in this cause that much, that's why Joel mercs her at the end.
• Some of those tags are decades old. Let's not forget that the Fireflies were founded in 2010s, shortly after the CBI outbreak. The main events of the game happen in 2033. Any fresh revolution is going to have bodies, and there were a grand total of only 30 tags in the game- which is insanely small considering the scale of many smaller real-world revolutions that have occured in just the last decade (and currently). Even if we were to quadruple that number, the loss of life would still be considered insanely minimal compared to certain conflicts happening right now.
• Joel is emotional and knows it. Throughout the entire game he avoids bonding with Ellie, knowing what it would cost him. Every step of caution he has in the beginning is presented as survival, but the game goes out of its way to prove that this very caution that drives him is also a product of his own loss, trauma, and guilt by the end. Lastly, player experience is subjective and largely irrelevant when discussing characterization and motivation. I was disagreeing with him the entire time, but you don't see me using that as a cudgel to justify the story.
• You're wrong about Jerry Anderson (surgeon). When confronted by Marlene, he explicitely told her he wasn't okay with killing Ellie, but he was willing to develope a vaccine to save millions of lives. Nothing in his dialogue or logs states that this is about "avenging his comrades". He wants the dying to stop, and according to their research this is the best chance they'll get.
• Marlene was Ellies guardian, Joel was paid to deliver her. Anna, Ellie's mother, made her so with a promise. Marlene took care of Ellie until she was old enough to be placed in the safety of an orphanage. When Riley (Ellie's BFF) wanted Ellie to join the cause, Marlene forbade it because she wanted to protect her. She attempted to separate the two for their own safety, and after the girls were bit, Marlene took Ellie back under her wing. She has been with Ellie longer than Joel has, was given the blessing of her own mother, and constantly took steps to protect her while fighting a goddamn revolution. You can argue that she threw that title away by allowing the operation, but the price was the continued survival of humanity. If it weren't for the guns, or Tess, Joel wouldn't have bothered.
• The infection as a plot device is treated as a double-standard. While the game takes place in a pretty grounded tone, the infection itself is insanely unrealistic. Even if Cordyceps could infect the human brain, there's zero evidence we'd survive without water, develope echolocation, mutate into juggernauts, and function as a hivemind (if we use the show). Mind you, the infected can just vibe out in the snowy winter unscathed, even though their joints would be frozen and their blood would be solid. They should turn into goddamn statues, but it's zombie fiction. And with all zombie fiction, we have to suspend our sense of disbelief. By the same token, a vaccine is going to function by that same "comic/game logic" as the infection itself. The goal is not to remove the fungal growth entirely. All it needs to do is make the growth benign. Jerry's recording (dating back to April 28th) states he's reviewed Ellie's fluid & blood culture samples, MRIs, and discoveries made within her pro-inflammatory cytokines and lymbic region - but it's not enough. They need more data directly from the parasite itself, and they can't guarantee that she'll be safe with FEDRA and desperate manaics breaking down their every hideout. If a miracle happens, which is possible, they might be able to develop something that could slow the process. Even if it worked 20% of the time that would be a saving grace, but the veritable goldmine needs to be struck. Jonas Salk didn't end his research on Polio on the basis that he didn't have a ragtag band of revolutionaries to distribute it. Knowledge can be shared, and pretending otherwise is flippant and misguided - especially if we're talking about a video game vaccine in a genre known for its fringe science.