Simple idea, a checkbox that says something along the lines of "Dot Trail on the Mission Map". When checked, (default), they show up. When unchecked, they vanish.
I've got over 97% of Cantha explored on my necro, and I've never had any trouble with the dots getting in the way. In fact, they help more than they get in the way.
"Map Makers" as in, fansite/quest help map makers?
Yes, I run a fansite GWDominion.com and the dots get in the way for maps of the Undercity, Fissure of Woe, etc. (of course, the maps wiping themselves when you leave also is a problem)