So, I brought up something similar to a third year law student last week. As he explained it, when the police arrest a drug dealer, the drugs are seized and tested for evidence. They don't get to keep the drugs, possibly destroy or sell them, etc. while the trial is pending. Likewise, in this case, the servers are going to be seized as evidence pending trial.
He also noted that a grand jury had been impaneled and indicted Megaupload (along with six individuals) and a judge had issued a warrant.
So, it wasn't just someone at the FBI or DOJ. It was a grand jury in the Eastern District of Virginia that indicted them. It is being prosecuted by a US Attorney. More than 20 search warrants were issued in nine countries. It was investigated by the FBI, the New Zealand Police, Hong Kong Customs, the Public Prosecutor's Office in the Netherlands, London's Metropolitan Police, the German Public Prosecutor, the Royal Canadian Mounted Police, and others. Megaupload and the named individuals will have a public trial.
I'm not saying that you should like it, but it is different from "feeling a lot like Russia". There's a certain amount of secrecy that happens in a criminal investigation to prevent those being investigated from being able to hide what they're doing (if they're doing something wrong).
I definitely had your reaction when I found out that the site was down and they hadn't had a chance to defend themselves. I think most of us see this as a civil offense - in which case, the seizure might not be justified (I use "might" because I'm not a lawyer). However, if you look at criminal offenses (bank robbery, drugs, gun running, art theft, etc.) you wouldn't expect the accused to keep that property pending trial.
We'll see how this plays out. If you don't believe what they did should be a criminal offense, even if they're "guilty" of it, you're not going to agree with any of what the governments are doing. You're going to think that they should be sued similar to what happened to YouTube and have the chance to defend themselves while operating. That's an argument to change the law and you won't be satisfied by the process no matter how above board it is. And I'm not saying that you're wrong - Megaupload does seem a lot more innocuous (even if wrong) than what we generally consider racketeering or conspiracy. I mean, if Megaupload continued, you're not going to have some kid getting addicted to crack on the street or gangs getting guns and causing violence in the community - some rich media company potentially loses a little profit. And I think that reality makes a strong argument that maybe seizure wasn't necessary. However, it's also important to know that there was a lot of due process in a lot of jurisdictions with a lot of different law enforcement working together on this one. It wasn't just seized because some unanswerable someone in a random agency decided they wanted to. Likewise, there will be a trial.