Over-prosecution is a technique often used by prosecutors to force parties into agreeing to a plea deal. By seeking to charge the victim with as many felonies and crimes as possible, they essentially blackmail their target into agreeing to the plea bargain, which is cast in a better light.
The goal of over-prosecution, is perhaps to make an example of the victim, to deter others from committing similar crimes.
However, the purpose of the Judicial system is not deterrence. It is Justice for all. The prosecutors should not seek to charge anyone with every little mistake they have made, nor should they use someone's history of civil disobedience as an excuse to over-prosecute.
It is the goal of the United States to bring about justice for all. Over-prosecution is not justice; it is tyranny