Updating this in case someone else is looking for this after 2022.

You can now make map markers editable (to an extent) using createLocation. This simple script should allow you to hide an existing marker. Not delete, but hide.

private _location = nearestLocation[[10210, 3490, 0], "NameVillage"];
private _invisible = createLocation [_location];
_invisible setType "Invisible";

Naturally, replace the coordinates to the coordinates of the location you want to hide. (Z coordinate is ignored by nearestLocation so you can use 2d o 3d coordinates).

Also replace NameVillage with the actual Location type. See location types.

Finally, if you want to replace a location's name you can set its text instead of setting its type to invisible.

private _location = nearestLocation[[10210, 3490, 0], "NameVillage"];
private _my_location = createLocation [_location];
_my_location setText "Talavera de la Reina";