The only reliable counter to a drone is likely another drone.
I suspect Peter F Hamilton got it close, in the Confederation series, with WASPs. They are space based weapon platforms. They carry a mix of offensive and defensive subsystems, and operate with swarm logic.
I could easily see a larger drone carrying a swarm of 1 shot micro drones. When close, some would be sacrificed to get better sensor data, others would go on the attack. Conversely, a defensive target would launch their own swarm. It's goal would be to stop the attackers getting a good shot on a high value target. It might also counterattack, either against the mother ship drone, or backtracking to find the launch site.
Jamming would also be part of this. A jammer could easily cut off the swarm from external data sources. Live satellite or remote surveillance systems would be cut. Point to point lasers are far harder, as are burst transmissions. Local sensor drones could easily punch short range data back, or paint targets, until they are destroyed by defensive systems.