When an emplacement is about to go down the squad could just evacuate and only the very reduced build cost would be lost.
That's the point. You make the emplacement itself a lower investment but in turn nerf it by making it rely on a garrisoned squad to operate. Because it's reliant on the garrisoned squad inside to do anything it's also vulnerable to anything that flushes squads from buildings. They'd essentially be the old UKF password-protected trenches with guns on them.