It should be obvious that the proper comparison is between the cost of the weapon used against the target, and the cost that the target will impose on you if you don't destroy it. That is, the cost of destroying a target should be less than the cost of not destroying it.
The story gives us no information on what the cost of not destroying that quadcopter would have been. Was it locating a critical installation that would be destroyed by artillery if found? Or did it in some way endanger a critical/expensive target of some kind? We don't know. All we know is the relative cost of the quadcopter and the missile used to destroy it.
Now clearly you can go broke using expensive weapons to destroy cheap and plentiful targets. The cost of your defensive weapon ultimately does matter. All that means is that you'd better find some other way of protecting your critical/expensive targets, so that they're not vulnerable to cheap and plentiful weapons. A more effective approach might be to cut off the supply, or destroy the source, of the cheap and plentiful weapons used against you.
My point is that it's not sufficient to look only at the comparative cost of your weapon and the enemy's target that you're defending against. You also have to look at the cost of not defending against it.