I imagine step one for prosecutors will then be to get the judge to specifically order the service shut down, due to hard caused to third parties or some other reason (whether valid or not). It's a common and vital tactic for prosecutors to seize funds of defendants so they can't mount an adequate defense.
I think the only way around that is to get laws changed, or have provisions in place to illegally host your service after it's been ordered shut down. The latter will probably just cause more legal problems.
As I understand it, the trouble is that money isn't evidence, necessarily (while Dotcom's server data would be) and civil seizure of money only applies to the proceeds of a crime. If you're a mob boss, you probably have lawyers and accountants working to keep the illegally-earned money out of your legitimate bank accounts.
I think the only way around that is to get laws changed, or have provisions in place to illegally host your service after it's been ordered shut down. The latter will probably just cause more legal problems.