Writing a hostile email and it being CC'd to the entire company -- depending on what was said, could absolutely be enough to be terminated.
He had his mental breakdown in Feb, the same month the email was sent. It's not that hard to imagine that the email was his "mental breakdown" and it being CC'd through the entire company is why Sony HR became involved.
Sony HR calls to get some information, and that's when he explains the situation, and more importantly; the sexual assault. The next day he was fired for the email, and was offered a $20,000 severance as long as he keeps the information of his termination private.
I'm not sure how HR works, but if they already have the go-head from Naughty Dog to let him go, whatever David tells them wouldn't stop them from firing him, right?
He absolutely could have been sexually assaulted, but the article now gives a new possible reason for his termination. Thus the "doesn't look good for David" comments.