C&Cs tend to be tougher than intercontinental ballista
The laser can smoke an intercontinental missile because they're light and live in aluminum tubes; melt the middle of that aluminum tube and it should become sufficiently unaerodynamic that its flight ends. The challenge is putting enough power on it for a short while to do that.
Doing damage to a building would require a lot more power / energy. It wouldn't be efficient to use a system designed to damage something small and fast-moving to damage something large and sessile, or at least large and dormant. The wasted optimizations bring along with them a lack of overall damage-dealing capacity. Although, the zero-flight-time ability does reduce the enemy's ability to defend against the attack.
Still, I assume the better way to destroy an enemy's command and control system, from hundreds of miles away, is to hit it with a bomb. (Either the bomb flies the hundreds of miles, or an airplane carrying it does. Have you seen any enemies physically deny us the ability to fly planes with bombs over their targets recently?)