Additional Info...
It was said here and elsewhere that only the LI pilots were "punished" so far and the traffic controllers passports were not seized.
The fact is that the traffic controllers are military, so they are not free to leave the country without permission.
In the eyes of the Brazilian justice they are being equally treated because they are all free to come and go inside the country (and it is a big country) and they are all not allowed to leave.
By the way, the traffic controllers were put on leave since the accident, they already hired lawyers and they blame the American pilots. The families already founded an association and it blames the pilots and the Union. I can remember a 1989 Varig accident over the Amazons where the pilots were sentenced to 4 years due to negligent behavior after 2 or more years of discussion...
In the present case, it is obvious that the ATC was incompetent, the control systems failed, the Legacy transponder failed and the pilots did not do their homework. They did not know the radio frequencies, they did not know the differences between Brazilian and FAA regulations regarding to loss of comm procedures and -- most of all -- they did not study the flight plan. If they studied the flight plan before they took off, they would know that the airway from Brasilia to Manaus has 2 ways and they would know that if they enter this airway in the wrong altitude they can hit something. That's the point, in the prosecutors point of view, that makes them chargeable of involuntary manslaughter.
The prosecutors will show this to the judge in 30 or 60 days and the pilots may be formally charged. I really don't know how the prosecutors will do, but the judge gave them much less time to reach a conclusion than it will take to the technical investigation to finish (10 months from the date of the crash).