Personally, I would fire this cleaner if i got that kind of message. Even if she actually had a point (which i don't think she did) she handled it very unprofessionally in my opinion.
Before our cleaner comes i do tidy, pick up stuff off the floor, do the washing up, throw out any trash on my desk etc. but our house is so tiny (smaller than a "trailer" or caravan) that no matter what I do it's cluttered. But she works with it.
The house is so small that by the end of the two hour block (minimum booking time per visit) she's looking for extra stuff to do and frequently offers to wash the outside of the windows, organise some of the more cluttered shelves, iron, tidy the desk, pull out the storage under the sofa, clean in it and put it all back etc.
Now that's what I call service!
I don't think that having the house virtually spotless is necessary but making it as easy as possible for her to do her job is certainly the best approach. However, a one-off "mess" due to having to leave the house in a hurry for a medical appointment, I think she should have cut you some slack. It's not like you left a weeks worth of dishes all over the house and dirty clothes and toys on every available surface. And it was just Once!