I believe the rat infestation occurred when the guys on the street became wise to what their superiors were doing.
Setting rules to follow, which seemed to work for a short while until, it was blatantly obvious the guys on top had no rules for themselves.

Look at Pete Casella, and old school guy who KNOWS the rules gets a retirement pass for whacking a boss?
Is there a worse violation in Cosa Nostra?
The commission is supposed to eliminate anyone who dared to try such a move.

I often wonder what era stuck to protocol the most? My guess is probably after Anastasia was eliminated and books closed but, what do I know?