"The reason [for the restructure] is because the franchises' teams can't support themselves so they are making the small people look after the big people," she said. "Everybody will have to pay more ... to support the Magic."
Mrs Thompson said Netball Rotorua had always received specialist coaching and umpiring help from Netball BOP but it was unclear whether that would continue from the new board.
Despite her reservations, Mrs Thompson said it was now up to Netball Rotorua to make the best of the situation.
"We've got to be positive, it's up to us to make it work."
Netball BOP coaching development officer Jodi Tod said the "end of an era' was sad but the Tauranga-based staff would continue as a Bay of Plenty zone outpost. She said at this stage they had been instructed it was "business as usual".
"We've been told to carry on with our camps and programmes in the Bay," she said.
She said one of the big unknowns was the future of Bay of Plenty representative teams - for many up and coming players a crucial part of their development.
"BOP Gold [the top side] will continue, possibly an under-23 side, but the age groups we are still negotiating what will happen."
Ms Tod said one possibility was for players to represent their centres, for example Rotorua, and inter-zonal matches could be held.
She said the organisation would be thinking outside the box to ensure the move doesn't negatively affect Rotorua players and would be working closely with Netball Rotorua in that regard.
The 2013 Magic squad member said she was keen to retain the pride in the blue and gold.