That's true. Personally, I'd use it as as an offensive weapon to contain forces, not to utterly destroy them. I don't like to completely ruin someone's fun.
Muslim had some interesting concept where the usage of WMDs were limited, and thus the RP went smoothly.
If I may propose a possible limitation, "Given that you have the capability to create or purchase the QCO, you can only use them once every __ days (realtime)."
This would be like 5-7 days.
This would allow for other tactics to be employed so that QCOs are uncommon, and defenses against craft that can deploy them can be put in place.
You could also go by the "no insta-hit" rule for long distances, where you say you launch it, and there would be a gap where the player can attempt to intercept or something.