In an awesome development, CCP Delegate Zero has already clarified this point:
“Once disputed territory between the two empires, the system remains under Amarr sovereignty, with the Gallente having rights to mine there as long as they sell a fixed amount of minerals to the Amarrians each year at cost price.”
Lore clarification
This makes perfect sense.
Given that the Federation had a good deal in the system already, the argument that these attacks are “false flags” gets stronger. The force that attacked the system had no hope of seizing control from Amarr. The only thing that could be accomplished was ruining the deal. Even as a “false flag,” the Empire would almost certainly be within its rights to terminate the deal - so the operation might actually be quite a success for whoever is manipulating us.