The real world equivalent of domain seizure isn't temporarily restraining a business from certain questionable activities. It is to fire missiles at the corporate headquarters the moment they are indicted, destroying the building, and then posting a billboard on the empty land saying how the company that used to be there and all of their customers are criminals even if they haven't yet been found guilty. If they are found not guilty, then, after more legal wrangling, they'll get the empty lot back. They are then "free" to resume their former operation.
If they open up, they might have trouble getting business if everyone thinks there are probably still rat turds in the food. So they need to advertise, maybe "change management", maybe change the name.
Who cares if the old domain is dead, if a new one can be set up that runs the same way and is just as popular?
I find that characterization both hyperbolic and inaccurate. An analogy I am much more comfortable with is seizing a business's physical store, locking the doors and keeping the key during the trial. I'm more comfortable with it because it smells like the kind of analogy a judge would make when interpreting how existing laws should apply to the internet.
So, can you provide an argument for why seizing the physical building is okay, while seizing the domain and servers is not okay? If you cannot, then what you propose would have to also apply to physical buildings, which means you're proposing a fundamental change to how seizures work before a criminal trial.
I find that difficult to believe. If tomorrow, the people behind MegaUpload were released, and their assets were released, and they were told they could go back to running MegaUpload as they had done so, I suspect they would, and the users would flock back to it.
Your claim is that websites require unique protection with regards to seizures. I have difficulty granting that, because if you seize all of the assets of any business, that business is, at the least [1], temporarily on hold. So, unless you can provide an argument for why websites are unique, then the process you propose would have to apply to all businesses. I have difficulty with that.
[1] I mean "at the least" literally, as a lower-bound. I don't want to get into a side argument about the likely fate of MegaUpload, since my point is that MegaUpload's fate is no different from that of other businesses.