What needs to happen is for large groups of people to go into these restaurants, make large orders, and then, cancel the order, making the statement that, “Oh, that’s right, this company turned it’s back on the Boy Scouts! I don’t want to do business here after all”
There is very little to be accomplished at the store level, were grunt employees are probably completely oblivious to the politics of any protestation you might make, and would be unlikely to relay that message to the people who need to know if they were aware of it.
Better to just cease patronizing them, tell every conservative you know, and then write, call, email the corporate office to let them know they lost a lot of business.