Four shuttles managed to transfer the entire crew of the two vessels to a secure Hangar aboard Terminus, where they were restrained and placed in the former produce cooler as a group holding cell.
Max hadn't considered the need for a prison facility, so they didn't have any proper holding cell aboard the ship, an oversight he would have to rectify eventually, even if it was just for these sorts of rare incidents.
The Reavers didn't usually try enemy crews in court or capture ships unless the crew couldn't afford to pay the ransom to make reparations. If they did, they would have more ramshackle ships than they did people by now. But these weren't Pirates, they were proper military ships from a recognized nation, so it wouldn't be proper to treat them like Pirates.
The fact that their nation was about to fall didn't help the odds of them paying to get their ships back either.