1. The US government has sovereign immunity (except where specifically waived by law) for virtually all its official acts, unless those acts violate the law or constitutional rights.
2. The supreme court has affirmed in a somewhat similar case, Kosak v. US, 465 U.S. 848 (1984), in which a set of paintings were detained (and possibly slightly damaged) by Customs officials. More recently, the core holding in Kosak was affirmed in Dolan v. US, a case regarding a specific waiver of immunity for the US Postal Service (though the lower court was reversed).
3. In a recent series of cases on criminal law (Medellin v. Texas, among others), a majority of the Court made it clear that they do not view decisions of the International Criminal Court as self-executing, meaning that they are to be followed without the ability for the Supreme Court to review them.
In other words, this is a real longshot. At some point, if no criminal case can be proved, the accused may get the servers back (and the users their files). But if convicted (or if the assets are subject to foreiture as the fruit of illegal activity), there's a good chance those servers are gone for good.
Besides, how would the FBI establish that the files were non-infringing and should be returned? In theory, the DMCA helps guard against this--had MegaUpload actually followed the takedown procedures, the government could have more faith that returning the servers to a surviving entity wouldn't put the same infringing content back online.
Imagine a scenario where your financial advisor has control of some of your money and also happens to be a drug dealer or insider trader. The police bust him and seize his assets, but because money is fungible they can't tell exactly where all the cash came from. Your money is frozen pending the outcome of the case and a determination which assets should be released. You can sue the accountant (he had a duty to you), but suing the government isn't going to get you very far. Not exactly the same, but analogous, to my mind.