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.