Well the minimap can simply be a translucent 45 degree tilted square outline with zero regard to topography but rather when you click on it it just moves your camera to that approximate location relative to your current Z-level and camera rotation.
Example: You are currently looking at the top corner of the map then you click on the rough area on the minimap that corresponds to the left corner and the camera snaps to that rough area to what ever accuracy the minimap is designed to be accurate to.
map graphics are optional, but micecraft does it with graphics (with a mod) so it should be possible in a 2 dimensional game.
Then how would you know where on the map you would jump to. Afterall you rotate. And whether being a blank square for clicking or not is a different matter.
Topography would have to be in place to distinguish the surface.
Minecraft, since it is 3D and you can look strait down; has an easier job to get the topography. Which most map mods out there, including the one in-game with map making; they all use what is there on the surface to draw a basic representation.
The hurdle that would need is to get the isometric converted to a simple overlay. Since there is 4 sides or views the main window can take, it is not fully 3D, but more or less 2D/3D combo. The illusion that things are such.
I think the seed and settings could play a part in this, as that would help define the mini-map; since really all it needs is a basic representation. I say basic as that is the way to keep it from adding to the lag that might pop up if was fully rendered. So the trick is to not actual render a map, but create a map from the seed and settings there of into a basic or simple representation that is just a flat image.
Done that was colors could represent different blocks used, so when a change happens, the map could be dynamically updated to the coordinates with the new color for what ever block was place. The key here though is how much to update the map; which also possibly could be a setting that could be added along side it. This way there can be an adjustment within game to how much time is used to process such updates.
Really the only thing the map itself has to pay attention to is the top most blocks or terrain. At least for when it needs to update.
So it is quite possible to do it, however I am pretty sure the coding for it might be a tad tricky in some areas, but should be strait forward at least in concept. I think.
Regardless this would be a lovely thing to have eventually, even if the feature I mentioned before I primarily use. Of course you would also have to determine; which could also be in settings, if the map will be static or rotate with the view as you rotate. I prefer something static, however you have to determine which way is north, but that could be simply already marked by the coordinates anyhow.