With only the first game's lore, it was both implied or stated that they were mostly hacks. A bunch of almost terrorists holed up in a hospital with a guy who knows something medical, so clearly that made them doctors and researchers. You could find an item that said it wasn't even the first immune patient they got, and they butchered the previous one with nothing gained and were about to do the literal same procedure on Ellie.

Literally, with all information given both to the player and Joel, there is zero reason to trust they know what they are doing. They skip every single attempt to ingratiate themselves to instead be assholes, brutes, or rush something.

There is a reason why Part 2 had to spend a huge chunk of its runtime on flashbacks, because they were literally all necessary for the huge retcon needed to even remotely make it a "grey" choice, let alone the "correct" one Neil keeps trying to say.