From what the article said, I think all fault lies with the passenger. As someone else pointed out, it's the FA's job to make sure all passengers AND bags are stowed correctly, prior to takeoff. All the FA did was ask if her bag would fit, and then made a very innocuous comment "oh, its smaller than I thought" She was only doing her job, and I don't see where she was rude to the passenger in any way, shape or form. Nor do I see where any apology was required.
The passener however, "DR.", was rude. esp. with her comment about being addressed as such. Unless the FA is a mind reader, she has no way of knowing that the woman was a dr. I think the airline handled things correctly. I may be biased as I work in retail, but it seems to me this was case of "the customer is always right" at least in her mind, when in fact, that's not always the case.