The federal government does have a process for this sort of thing, if they seize an alleged drug dealer's house and that house has a mortgage the United States Marshals Service will pay the mortgage. If they seize cars, furniture, other assets the government is responsible for the storage of those items until the case has been resolved. [1]
I would guess that MegaUpload's lawyers will make the claim that the data on those servers is critical to their defense and must be maintained. That is probably an accurate claim, DotCom will want to present evidence of compliance with DMCA notices, counter the claim that a "majority" of the content was under copyright, etc. Best case for DotCom would probably be that his lawyers argue for retaining the data and the judge lets Carpathia destroy it anyway. That would give DotCom reasonable grounds for appeal.