I spent an hour making a decorative floor, just to accidently flood the room. Now I have to destroy an hour worth of decorative work, because mud cannot be cleaned.
There should still be a way to manually ask dwarfs to clean it. I do think that mud should never be "auto cleaned."
Making mud act like blood, spilled drink, or vomit would allow for the option of cleaning through a selection button. Once fungus/moss starts growing, or it is turned to farm plot. The mud would be able to replace the tile it is on.