I see the Construction Yard as having 3 abilities:
Passive: Slowly heals buildings, exactly like unit regen on Elite.
Active: Allow for other buildings to be rebuilt if destroyed 1 time each during a match, at high cost (eg, 20,000 Credits)
Additional Commander power: Allow for defensive buff on building which increases it's armor for a limited time (exactly like defensive buff currently but only affects the building) [this commander power is disabled if Con Yard destroyed]
In this way, there are many advantages to having the Construction Yard active, but if its destroyed, the team isn't penalized for not having it active.