missiles are bad and they should feel bad. The word literally means projectile. We have those in the game, they're called ranged attacks.
This is what I would do with Missiles:
Remove them entirely and use their art asset husks as animations for an improved city attack (if possible).
Remove all missile units
New Building: Missile Silo
Available at Rocketry
Requires Arsenal
2250
10
+1 City Attack Range
+15% city attack damage
Changes city bombardment animation to the guided missile
Move Military Base to Atomic Theory
There, now you have guided missiles that people actually will use. They're a late game bonus that makes city strikes hit up to 5 away with red fort.