Missile costs 1 citizen, but as it selfkilled after attack, maybe it shall return 1 citizen to the city where it was build. I think it will better fit the balance, as you still cant spam too much missiles and they will be much more useable. 

Also they should be able to be launched from rocket cruiser imho

What if it would need just at least tot people in the city to build it but it wouldn't kill them? (Something like having 20 pop in the city and at least 5 researchers; I dont think that a city full of District but poor of people whos only inhabitants are just a handful of farmers might actually have the prerequisites to build missiles. I think that this philosophy should affect also many other aspects of the game in order to make people more of an actual "resource" too, in order to break, especially in late eras, the paradox of having huge cities nearly non populated which are still able to move your empire)

Especially now it is possible to do limited units, so maybe they really somehow could depend on population/districts, but at least they shouldn’t fire own citizens, as I imagine it like this:

Ahahah, yeah I agree. That's the same thing that passed in my mind when I first thought about it.