I think Manfred was not allowed to penalize the players (due to the MLBPA), which is why they were granted immunity. The most he probably could have done without legal backlash was vacated the title, and I think that would have solved a lot of the PR mess that followed, but he decided not to open that box, and it has cost him dearly in the court of public opinion. Honestly if he suspended no one and just vacated the 2017 title, I think all of this blows over. I'm curious to see if he decides to change his mind and vacate it now that he's found himself in a PR mess, but I still doubt it because as mentioned I think a lot of teams are electronically cheating and he wants to bury this as quickly as possible.
Regardless I don't know how in the world he could not stop himself for verbally degrading the World Series trophy in a sport that he's directly responsible for improving revenue. I used to sympathize with him because I think fixing baseball is not going to be easy, but it seems he's done everything wrong or shown little/no effort in trying to improve it. Even his words show no love for the game.