I'll bet it's either in the options page under map/minimap or the right click on the map menu under the show heading.....something to the extent of saying "show kill icons" is what you are looking for.
Richt click your map, select Show... and uncheck Show Kill Icons.
What the skulls represent is all the places you've died and, possibly, all the places you've killed another player. I don't do PvP, so I wouldn't know.