My first thought is just a bummer of a coinsidence.
For starters, it should be impossible for a controller to break a pipe. The only thing the controller does is operate a sealed selinoid that opens a piolet hole in the valve. The valve itself uses mechanical means and water pressure to actually open the valve.
As for the lightning, I wouldn't think a strike at the controller could cause pipe damage... not given that the pipe is plastic, and surrounded by soil. But then having said that, lightning is such a huge uncontrolled burst of raw energy, it could do anything. After all, if lightning struck the controller, the lightning could travel down the wires to the valves, and then through the pipe itself trying to get to ground. After all plastics are not non-concuctive, they are just VERY LOW concuctance (extreamly high resistance). But extreamly high resistance faced with extreamly high voltage can still result in current flow. But if it was the lightning, then because the primary pathway would be through the control wires, I would expect damage at the valves (especially at the selinoids) before seeing damage to the pipe beyond.