I also used markers that way. Now I feel smart for guessing it's purpose! 
But once I realized markers don't have nor thermal vision nor camouflage revealing, I gave up trying to use them. Just like handcuffs.
The markers are cheap disposable units. No penalties if they are lost in combat. Also not meant for
every mission, but only on a selected few, at the discretion of the player. Eventually, once the troops have access to better armor and weaponry, and are in great numbers, markers are used less and less.
The main problem with markers is that they are ridiculously slow. It takes at least 2 whole turns to place one marker.
It weights like 9 units. A strong soldier can carry one in a backpack. But the best way to use it is to relay it across the map. Or at least that's how I found myself using it. One near the stash tile picks one and throw it at one soldier, they, pick it up and deploy it or throw it to another further away. Remember, markers are mostly to secure coverage on a partially conquered map, where you don't really want sneaky enemies attacking from behind.
In "Enemy Within" there also was something like markers, but they were in the form of throwing items, which made them somewhat useful.
Yes, the idea of a throwable marker, like a javelin, was at some point considered. It may be OP. But it can be done.
And also there is whole 2x2 unit that can only place markers (few tiles away), but has technological level of hovertanks! How useful is that thing? 
I think the hovertank main purpose was to deploy flying drones, as a nod to Starcraft
The markers clips were mostly used as a "filler". I suppose I can implement a sort of "manual" dispenser. An agent may pick up and kneel to use, like a mortar, but fire the markers instead of explosive rounds.
