Fighting nano bots with nano bots would not work because it would be like fighting fire with fire. The enemy nano bots would greatly outnumber any countermeasure that could possibly be deployed due to the amount of time a response takes. The only way you could defeat a swarm is with bots that replicate much faster, but you won't have that opportunity because your tech is the one turning on you. Any bots you deploy against it would be identical.

For example, China messes up and a swarm is consequently consuming the country. They deploy the functioning bots, but their capabilities are the same as the foe and are already outnumbered by a huge margin due to exponential growth. The US has superior bots, however by the time the threat is realized and they can properly deploy the countermeasure, it is already too late. As for magnetic fields, you would have to destroy a sizable portion of the planet to get rid of all traces of the bots.