The Capital is usually a place where many vulnerable units are located, especially auxiliaries and FRDs. While auxiliary carriers should always be escorted, to prevent their destruction during a drone raid, there is little that can be done to protect other auxiliaries and FRDs.
To stop this, you must combine the effects of rules (320.355) and (537.32). Rule (320.355) allows intercepting groups made up entirely of fast ships to select two numbers for interception and an Electronic Warfare Network allows an extra group of interceptors. By having two groups made up of all fast ships, and one extra group allowed by the Electronic Warfare Network, the defender of a capital can ensure that a drone or special raid is always successfully intercepted!
While this will not prevent the enemy from accomplishing their mission (a drone raid on slow units is almost a guaranteed kill), it will result in the attack being more costly to the attacker.