A few thoughts (some of which may be correct):
They can't punish the players until they have an agreement with the players association giving them authority to punish players for using technology to steal signs.
Beltran was a player with the Astros, so he can't be punished for what happened in Houston.
Houston waited to fire Luhnow and Hinch until MLB issued its report and fines. MLB skewered Luhnow and Hinch for not maintaining the integrity of the game, which surely is part of their contracts with the Astros. Since they violated their contracts, the Astros could fire them without having to pay them for the remainder of their deals.
The Mets won't fire Beltran for what he did as a player in Houston. He did not violate his contract with the Mets. Had this come out earlier, they might not have hired him, but that's poison under the bridge.
The unofficial rule on cheating in baseball remains the same: It's okay to cheat as long as no one notices or it doesn't work.