Okay, let's assume for the sake of argument the "Worst Case" scenario for everyone involved, based on the evidence "leaked". This is far from factual -- just what the "best possible case" the FP would have:
Rookie FO on his first flight with the company, and with his bosses in back, fumbles when told to ident, and somehow shuts off the transponder.
ATC is watching the football match, and doesn't notice the transponder problem.
Both sides make a halfhearted attempt to establish radio contact.
After impact, when the Legacy crew turns to squawk 7700, one of them says "Oh ****, the transponder's in standby", and turns it back on.
So, if this were the case they had, who would get what out of it?
In any reasonable country, even this scenario wouldn't result in criminal charges, except perhaps to whoever setup the policies by which ATCs operate (and even in reasonable countries, those guys are well protected): there's no clear reason why the transponder was turned off, and no other evidence to suggest this was a conscious error, or one that occurred through willful incompetence.
Aviation Safety is severely damaged in Brazil: if you're gonna make a mistake and turn something off, better start with the CVR; and with a couple of controllers in jail, you think any future ATC tapes are going to survive without damage?
On the other hand, the provincial FP running the case becomes a nationally known figure. Perhaps noting how Tsolakis flight, catapulted to regional fame as the head of the Greek investigatory board inquiring into the Helios tragedy, the Brazilian Federal Police are making sure they be the focus of attention, not the investigators.
And that's the "Best Case" scenario, assuming the absolute worst of the pilots and controllers.
In short, it's a political game with very few winners, and millions of losers.