He's got a point. Ellie's story remains rather unresolved at the end of Part 2. There's a definite redemption arc for her in a potential third game. Druckmann won't be able to resist doing a trilogy. he's way too steeped in cinema to pass the opportunity up to do his Return Of The Jedi, now he's done Star Wars and Empire Strikes Back. Abby's story is done, though. She won't be back.
Also, she's not really immune, and they have to do something with that twist:
These theory videos are usually horseshit, but given how much research Naughty Dog did into cordyceps, I well imagine them going for this kind of twist. (If you can't be bothered to watch, essentially Ellie is infected with a different strain of cordyceps that fights off the kind that turns you into a zombie. This is actually based in the science of how the fungus operates in the real world).