Zero fathers had problems with this.
Even before I became a father, I 100% agreed with Joel.
(1) Ellie never explicitly stated she was willing to die for a cure. She didn't even know that was a possibility.
(2) The Fireflies wanted to take away her right to bodily autonomy. They never told her they were going to kill her and pick her brain apart.
(3) Even if the had told her, she was 15 years old. She's not old enough to make those kinds of decisions.
(4) The entire game is you watching the Fireflies fuck everything up, over and over. They were completely incompetent. They would never have been able to pull off a global vaccine.
(5) Expanding on point 4, the Fireflies have possibly the only immune person on the planet in their research facility. (I say possibly, because there could be other immune people. We don't know.) They essentially poke her with some sticks for 3 hours while she's unconscious, can't figure it out, and then decide to just chop her up. Fucking idiots. She should be studied for literal years.
Finally,
(6) There's no such thing as a vaccination against a fungal infection. It's factually impossible. The Fireflies, once again, prove they don't know what they're doing or what they're talking about.