I liked that episode, it definitely explained some things from earlier in the season that irked me. Season 1 Joel/Ellie can really tug on your heartstrings.
However, I thought the whole point of Joel's rampage in SLC was to save Ellie from being a lab rat for the rest of her life and likely being killed in the process. She had no idea what was going on, and the hypothesis of creating a "cure" with her blood was far-fetched at best. He was saving her from the insanity of being some stranger's guinea pig in an organization full of zealots who thought they could fix the world, it wasn't completely an act of selfishness.
If all the Fireflies needed was blood, then they wouldn't have knocked her out and taken her to an OR. They would have started with a simple blood draw every day to build up supply to work with. I thought he recognized how their plan with her wasn't adding up, and he saved her from what would be a tortuous existence, thus justifying the rampage to some degree.
I'm sure it's hard for him to talk about it all, but why doesn't he defend himself? It makes no sense to me how he's completely disarmed when discussing it.