My gut tells me so much money went into this multi-national synchronized operation that no judge in his sound mind will let all charges go. at least they will have to break even.
Now, since as you say, this was a large multi-national operation, I don't know if all those charged will be extradited to the USA, or if they'll be tried in other countries. I really have no idea about laws & procedures around the globe, but if they are extradited to the USA, I wouldn't count the MegaUpload folks out just yet. It's probably very dependent on how much of their assets are frozen, which will affect how much of their money they can spend on legal representation. (I say unfortunately, because it seems to me that in an ideal justice system, everyone should have the same level [high!] of representation, rather than some being able to "buy" better lawyers).
In the USA at least, much of our government could function nearly the same regardless of if our market system is completely laissez-faire capitalism, or hardcore communist. In fact, you could argue that government and its' systems, like the judicial system should be completely devoid of any possibility for profit motives. Since, as saucetenuto states, those undermine the system.
Now, I don't want to get into an argument about whether good lawyers deserve to get paid better than bad lawyers, etc. But I don't think I'd want to meet the person who sees the justice inequality between rich and poor defendants and thinks "All is as it should be."
But outside of that, it's not up to the judge. It's a criminal case, and they will be tried by a jury. If they're convicted, the judge will determine their sentence. But it's not up to the judge to determine their guilt. (Unless the defendants forgo a jury trial and elect for a trial by judge, but I doubt they will.)
The comparison in this case might have the prosecutor go after some lesser charge just to stick anything in order to justify the huge operation in the first place.