I think there is sufficient differences in the final release version of ellie over the original early designs for it to avoid legal parties.
But at the end of the day, Naughty Dog did, quite obviously, use Ellen Page's likeness when modelling ellie, even if it was only a placeholder. I'm kind of surprised by this, it sounds like Ellen wasn't even consulted by Naughty Dog and if that's the case I can see how this could be a problem for Ellen.
It depends how the matter is judged... from the perspective of an entire production process or by the final product.
I doubt this will go beyond some letters/calls to and fro, but you never know.
EDIT: I'd also like to note that the coverage from this site seems to paint it as a far worse issue then Ellens initial reaction. As far as I remember she just said, "I should probably be flattered, but (because I'm currently in another game) I'm not sure* I appreciate it".
*I can't remember if she was definitely unappreciative of it, or conflicted.
That's a far cry from being a "VS" scenario. Even so, it is at naughty dogs feet if this does explode, but given the success of The Last of US, I can only see Ellen being torn apart by angry fans.