When somebody is injured or suffers some sort of financial loss as a result of an accident, restitution must be made... somebody has to pay. That's a given.
Criminal prosecution of pilots is one way to make such a payment. But it is not the most effective. I personally do not believe that putting the pilot in jail will increase the level of safety in aviation.
Civil litigation seems to be the best compromise, in that victims are compensated, investigators get their evidence, lessons are learned, and pilots don't spend useless years in prison.
In addition, financial penalties such as those imposed by civil courts hit the entire system which produced the accident, one way or another, instead of creating a scape-goat out of the people who were, at most, only the last line of defence before the accident.