Of course you'd let them do it if it was you. But if it was them on the table, you wouldn't let it happen if you really cared about them.

Also Joel did not kill "dozens of unarmed doctors". He canonically kills one and that's Abby's father, solely because he is the only one who knows how to develop the cure from Ellie's brain, and is thus the reason they will never stop pursuing her. Technically, he wasn't even unarmed since he threatened Joel with a scalpel.

As for the rest of the Fireflies, they were an organized terrorist militia group, not a bunch of unarmed civilians. Claiming Joel was on a rampage against a bunch of defenseless civilians is just false.