I really think they should just play the games with who they have available (bring up as many AAA guys as needed). Serves some sort of punishment for teams as well as gets those games in.
Ironically, the Marlins had their best season since 2003 after having a massive outbreak and deliberately flaunting the rule. The Cards were another team that broke rules on the road and had an outbreak, which is probably why 85% of the team lined up shots down in Florida.
It's a long enough season that these can be treated as rainouts. If it is individual violations rather than team, or no violations and just bad luck, then forcing a team to put on a non-major league product is overkill, I/M/O. Who knows, it might have been an asymptomatic cleaning crew member that coughed in somebody's room that started this.