I disagree, the BBC has shown itself more than capable of getting shot of people who were to troublesome or too costly in the past. Nobody is indespensible, not even Moffat.
But nobody is saying she was fired. She quit.
The BBC have made their willingness to give Moffat a lot of leeway pretty clear over the past two years.
But is it a case that she jumped before she was pushed? Is it that she felt she could no longer work with Moffat or is it some other reason; hell given she's moving to London this might even be a family related decision that has bugger all to do with Moffat/Who