This forum post, "How to remove the wallhack tagging when using the camera" from the Ubisoft forums, describes a method to disable "wall hack tagging" (seeing tagged enemies through walls):
Open the FC3.dll and/or FC3_d3d11.dll (depending on what you use) in any hex editor.
Search for the following hex array:
53 68 6F 77 54 68 72 6F 75 67 68 57 61 6C 6C 73 41 6C 70 68 61
Change the last value from 61 to 6F, so it reads like so:
53 68 6F 77 54 68 72 6F 75 67 68 57 61 6C 6C 73 41 6C 70 68 6F
Lastly, do a search for the following array:
53 68 6F 77 54 68 72 6F 75 67 68 57 61 6C 6C 73 00
Change the second to last value from 73 to 6F, so it reads like so:
53 68 6F 77 54 68 72 6F 75 67 68 57 61 6C 6C 6F 00
Essentially, you're renaming the commands ShowThroughWallsAlpha to ShowThroughWallsAlpho and ShowThroughWalls to ShowThroughWallo, which nullfies the commands when they're called.
For hex editors, see: http://superuser.com/questions/14465/hex-editors-for-windows
There is also a mod here that claims to remove wall hack tagging.
I found those from this thread, "Mods for Far Cry 3", in the Ubisoft forums. There are also a couple of mods or compilation mods (like this one) there that have a feature of removing the mini-map or enemy positions in the mini-map.
From the Far Cry Nexus, the mod, HUD annoyances fixed, claims to remove enemy icons on the mini-map:
This mod currently replaces the textures used for the minimap elements and the camera HUD elements in order to improve gameplay and/or remove distracting visual elements. The minimap remains intact because I think functionally it is fine, but I have removed the icons for collectables and enemies from displaying, so that more exploration is needed.
Also from the FC Nexus, there are compilation mods (includes many features) that will either remove wall hack tagging or disable or change the minimap to not include tagged enemies:
Greetings to Malmo
Legit Far Cry
Sleepingwsirens Modpack ReDux