Prosecutorial discretion is what makes it possible for your torrenter to not get such an inane charge.

How would you design the system instead?

That's the crux, isn't it. It's easy to point out problems but solutions are more difficult.

One of the things prosecutors frequently do is load up suspects with dozens of frivolous charges that wouldn't stick in court, to terrify the stupid into accepting plea arrangements. I think we need to look first and foremost at tightening up the procedures that facilitate indictment, under the current system you can indict a potato. At least some level of hard evidence of guilt or intent should be required to acquire an indictment/formal charge. Grand Juries shouldn't be rubber stamps for whatever charges prosecutors want to levy, they should act as a check and balance in the system.