I can think of one way to make it work without a client-side download.
Each person has a different list of marked buildings. The same building can be marked by multiple people, you can only remove buildings that you have marked. When you mark a building, the server sends a message to you alone: "You have marked the [buildingname]" and the corresponding: "You have unmarked the [buildingname]." To top it off, '/marklist' will give the client a list of buildings they have marked. Identical buildings get listed as a number, eg. 3 Turrets marked.
This is pretty much the only way I can think of making markdecon work without a client download. Then again, '/marklist' is a good idea on client-side mods anyway.