NPCs have always been slightly tolerant of friendly fire (and the closer you were to being Allied with them, the more tolerant they were), but they'd still fine you if the damage is above the threshold. It's my understanding that they've merely upped the threshold for damage before the bounty kicks in.
So if you're flying a death-dealing hyper-engineered horribly beweaponed personal battleship, you'll still likely get penalized for accidentally hitting a friendly, because your weapons are so lethal. My barely-engineered popgun-boats that take several minutes to kill an Elite NPC have hit friendlies in CZs and nav beacons since 3.0, and they've just told me to watch my fire and I carried on. No penalty.