Look at Vegapunk's face in 1067. "There's something I have to give her." Dude seems pretty serious.
Vegapunk talking to Bonney about the necklace: "He said it's a protective charm."
We know from CP0 that the Command Order for the Pacifista is:
Gorosei
Vegapunk/Satellites
Sentomaru
Anyone with a Control Chip
If that's the case, then, I believe Bonney's Sapphire necklace contains a Control Chip that gives her the highest level of authority over the Pacifista.
Once Vegapunk realized Bonney became a pirate, he developed this Control Chip to give to Bonney behind Saturn's back. If the Pacifista were already programmed to respond to Control Chips, programming a Control Chip to have a higher authority than the Gorosei and then programming the Pacifista to recognize and respond to it shouldn't be hard at all for Vegapunk, and since Vegapunk is constantly modifying the Pacifista, it would be easy for him to perform this switch without Saturn noticing.
No idea why Vegapunk wouldn't tell Bonney this, but, whatever.
Anyway, this would be interesting, because it means if Bonney's necklace is destroyed, she'd lose control over the Pacifista. Either way, even if she has full authority without a Control Chip and is just above the Gorosei naturally in authority, she'd lose that if she fainted.
Now that Saturn knows Bonney is in control of the Pacifista, she'll be the biggest target on the island, as the Marines need to take her down so that Saturn can regain control of the Pacifsta, like when CP0 took out Sentomaru to regain control of the Seraphim.
We have entered the "hunt down Robin" Ohara section of Egghead, where Bonney is now the most wanted person on the island.
This famously led to Aokiji helping Robin escape after defeating Saul... a Giant.
Oda's cooking something.