Yes, it is possible that lighting did hit the pump. If it did its a goner.
But, there may be some hope. If it is a 2 wire pump,(no control box) forget it.
If it does have a control box, there is a chance, that the capacitor stopped the lighting before it got to the pump.
It is a slim chance, but a chance none the less.
Depending on the size and depth of the pump, it could be anywhere from a few hundred to a few thousand dollers to replace it.
That is hard to answer without more details about the pump and well itself.