Janeway never pardoned anyone.
Never had them work off their debt to society or face trial to become vindicated or pay the price.
Admiral Hayes from Life Line assumed she locked them all in their rooms at night.
As soon as they the cross the Border into Federative space, Janeway gets proper relief and the Maquis are deposited onto the nearest penal colony because they are still accountable for all their cirmes.
If the Maquis assume different, they're kidding themselves.