My suggestion is when players test positive, they go right into quarantine and you bring up a replacement from the reserve squad that was created specifically for that purpose. If you have 18 guys test positive, then bring up 18 guys and that's who you have to play until the infected players test negative for 72 hours or whatever. That's the penalty for not getting your players to act responsibly - you have to play with mostly AAA guys for a week or two. If that knocks you out of the race, well, too bad - you should have done a better job of stressing the importance of responsible behavior. The Indians did.
I think the issue with this though is the incubation period of the virus. When you have one positive test, it's a waiting game on how many more you will have. For example, on Sunday, the Marlins had 4 positive tests. Sure, they could have just replaced those 4 guys with AAA reserves, but the 9 guys who will test positive the next day, and the 6 more guys that will test positive 2 days later, have now continued to play an opponent infected and have now exposed the AAA guys.
I think what we've seen with the Cardinals is a pretty realistic look at the way this turns out. Play is paused for couple days to let the incubation period catch-up, and those positive players will be replaced by reserves when play resumes. The season is either going to need to be extended to tack on those postponed games, or they will just need to go off winning percentage. With the way this has gone so far, I would not be surprised if every team experiences positive cases at some point, making it a bit of equalizer if it comes down to winning %.
This is why, in my opinion, the bubble is the only way playing sports will work. The environment has to be completely controlled to reduce the risk of infection and spread. Or, the development of an at-home, instant COVID test, like a pregnancy test, that is to be taken some pre-determined time before a game starts would be really helpful. A player cannot play until the results come back negative, just like a piss test for drugs before a UFC fight. That is a lost cause for the 2020 season, though.
Edit: ESPN mapped out the typical day for an MLB player under protocols, and by their estimation, a player comes contact with 63 players/staff in a given game day. I hope I am wrong, but I am just not optimistic that this will work.
A day inside MLB's COVID protocols.