It's worth nothing the co-presidents of Naughty Dog issued a statement saying
However, we feel it necessary to clear up a very important point that was unprofessionally misreported when the story broke. Bruce Straley and Neil Druckmann were NOT involved in what transpired. It was very upsetting to us that dozens of stories were run, linking back to the same hurtful accusations in the original report. As co-presidents of Naughty Dog, we are responsible for all studio affairs.
Here is my 2cents copied from the gaming website I use(CVG)
To take either side of this situation is foolish there are no facts other than she no longer works for Naughty Dog and in the absence of evidence you cannot put truth behind the speculation.
As far as I'm concerned this article story is no longer about someone leaving a company but about a supposedly credible company that is to say IGN circulating potentially harmful accusations. It would be different if it was a small games site aiming for clickbait as it would be called out as such but as "major" site not only reported it but broke the story it lends the IGN credibility(for whatever that's worth)
Now if Amy comes out and says it's all true(even then if the split isn't amicable there will still be a he said she said aspect to it all) I will appologise for this rant against IGN but until then I chose to believe that IGN are following Tabloid Journalism 101 which means that everything they say(especially their headlines) should not be taken as fact and they should certainly not be trusted as the only source of a news piece(which they are in this case)
/rant
I'm sorry I just really hate speculative media