This isn't some sort of reveal all feature. In case you haven't noticed, when you first enter a planet, everything is grayed out, and all you see is the place you entered from, uncovering that part of the map. The fact that quests are shown to you on the map isn't taking away from the exploration value, far from it.
You still have to go to each individual place and scale hills and mountains, trudge through sands and deserts, to get to each quest. IF, every single quest could be completed without moving your character at all, that would take away from the exploration value. But in this day and age, people don't want to make their own maps anymore, or spend hours figuring out where to go on one insignificant quest.
If you don't like the map markers, just ignore them, don't look at 'em. Do you think BioWare would make the profit they are currently making if players had to look for each target? It just makes no sense to do so in 2011, almost 2012.