Deciphering the codes is not the issue. Using the camera feeds to watch the codes via replay is the issue. In 1961, the use of any "mechanical means" or outside source for stealing signs was banned by the NL President Warren Giles. But players were, punished for it long before that, going back to 1901 when Phillies third base coach Pearce Chiles put his backup catcher in the centerfield bleachers with binoculars and ran a cable underground to the third base coaching box so the player could send him electrical impusles he could feel with his feet. He was caught mid-game because opponents noticed this perennial puddle in the coaching box (used to amplify the signal) even when it had not rained for weeks. Yes, opposing player ran over there midgame and started digging up the coaching box!!
So this was already deemed illegal. Steroids, for which players do get banned, were not made illegal until the early 2000's, unless the drug in question was already illegal itself.
Stealing signs by decoding them live - or looking for tells and pitch tipping - is still legal and was never banned. Just using live game feeds to decode them was.
As for changing signs, that has always been done. Usually as part of the set up. It can be something simple like "follow the two" where the sign after a catcher flashes the two is the real one. Or something more complex like "balls plus one" where the relevant sign changes with the count.
Of course, all of this was also much simpler when players only spoke English. But as MLB gets increasingly multilingual, the techniques for communicating have to adapt as well.
Just wait until some team employs some hacker to intercept the PitchCom transmissions!
Bottom line - Cora broke a rule. I used to think he was punished accordingly. I'm not so sure anymore. They ddi revamp the whole way signals get transmitted now because of him...