Well, my feeling is, that this is diffcult to avoid - if it is in the original datas (god is smoother in this case). How can any filter know what is still wanted and what is an artefact? But you can try "erosion" in the terrain editor. There you can smooth whole terrains - or you can try to smooth parts of the terrain with the brush, using "effects" and select one of the erosion effects.

One day your ship comes in - but you're at the airport.