Her problem isn't that she messed up. Her problem is that she doesn't understand her own business. If she had a long history of honest publishing and the story

Her problem isn't that she messed up. Her problem is that she doesn't understand her own business. If she had a long history of honest publishing and the story was that she had two browser windows open, one with a Creative Commons licensed article and one with an unlicensed article, and simply copied from the wrong window, that would be messing up. Not even knowing that copyright is the default state of a written work is not messing up. It's utter ignorance of a fundamental rule in the business of publishing. You can't make something like that go away. No amount of apology is going to change the fact that you don't have the requisite knowledge to be in the publishing business. The only correct response is to go back to the drawing board and learn your shit before you come back to work.