You can't cancel that. With only the distance information in D, the mds function has no way of knowing what is up/down/left/right or north/south/east/west etc. The axes and directions that the algorithm produces are based on minor numerical quirks in D (that seem irrelevant to us).
For example, look at the map output in the first example on the cmdscale documentation page--north/south and east/west are both inverted relative to the real world locations of these cities as we usually display them on maps.
What you can do is to rescale the output coordinates Y that you get from cmdscale. For example, multiply by -1 along one dimension to reverse the picture with respect to that dimension.
