Okay right off the bat

Joel's decision to save Ellie, or rather, to murder a load of doctors who were planning to use Ellie's immunity to create a cure that could have saved mankind, has always been shrouded in a level of ambiguity.

Let's call a spade a spade: Joel killed a lot of people who were trying to murder Ellie. I mean if what Joel did was murder, then killing a kid is also murder.

"Now, is our science a little shaky that now people are now questioning it?

People were questioning it from the get-go why these doctors were chomping at the bit to kill Ellie immediately rather than try other approaches with her first before resorting to death. Like a biopsy. Ever heard of a biopsy? Doctors certainly should know what a biopsy is. Try a biopsy first instead of chopping her whole brain out, holy balls.

I don't care that much about whether the Fireflies could pull it off since Joel certainly didn't care.

But don't forget: anyone saying that Joel deserved to die is implicitly saying that Ellie deserves to die.