Yeah, she literally years later after a shit ton of trauma "consents" to it, but I can guarantee if she was asked when they got to the hospital she would at least hesitate if not refuse.

Its why they had to create a DLC to give Ellie a bunch of suicidal guilt to try and justify it, which is still not acceptable "consent" in any other discussion.

They literally have to break all their various rules and principles regarding informed and enthusiastic consent just to say "let the teenage girl be butchered for the greater good maybe."

Ellie's consent should never have been a factor. She was borderline suicidal at that point, convinced that it wasn't worth living in such a rotten world where everyone she ever knew and cared about died. The last thing she needs is to have people start drilling it into her head that she needs to die, that she has to die, and that the whole world depends on her dying. People who, likely only a few hours ago, were ready to kill her anyway just for her boots.

As someone who cares for her, it was indeed Joel's moral obligation to save and protect Ellie, both from the Fireflies and from herself.