The doctor pulled a scalpel on him, and Marlene had Joel escorted out of the building and was begging for her life. As soon as Joel cleared out she would've began hunting him down, their is no way she would let the potential cure escape her.
A doctor with a scalpel is hardly a combatant, more like a non combatant clingign to a very ineffective weapon against a guy who just went through a bunch of heavily armed soldiers. Kinda stabbing him in the throat with his own scalpel seems more than a bit excessive for a an egghead in scrubs. Also, the fact tha the is murdering a doctor kind of a dick move. Also Marlene literally offered him a peaceful solution, if she had simply continued engagin him withviolence it owuld be one thing, but she pulled her hands up, proposed to talk it out with him and he just shot her in the stomach and then in the head as she laid on the ground.
Also, what was he actually stopping? didn't he state he was only doing it because Ellie didn't want to go through with it? was he just preventing her from even making the choice if the chance presented itself again? He also makes her never tell anyone she is immune. Seems like he just wanted to make sure she never even got the chance.
Which was all pointless because he killed the only person who even had a working hypothesis of how to make a cure out of Ellie's brain fungus and the other Fireflies didn't even bother going after him afterwards because basically their entire mission had become impossible at that point.
And again, this immoral actions is what to me makes him an interesting character. I actually was kinda bored with the story of the first game until the curve ball of the choice Joel makes comes, makes the entire adventure have a completely different meaning as basically the backstory of an anti villain.
Him dying at the hands of the child of one of his victims after he settles down and starts redeeming himself is very Western-y set up as well. Also the kid hero of the first game going down the path of turning into something similar as well while dealing with their feelings on learning about the past of the person they loved as a father is also an interesting set up. No idea why so many people are acting as if Joel is just killed off and forgotten when the entirety of the game is about the effect his death has on both Ellie and his killer.
Don't know how well it pays off just yet, but so far it's enjoyable. Altho I am not yet fully sympathetic of Abby, Owen on the other hand seems like the more sympathetic of the WLF gang but well... after playing through Ellie's half we know how that turns out.