It is not the flag of the Republic of West Florida. It is a flag used by the Confederate States of America. That is the primary association it has in Mississippi history. The Republic of West Florida existed for 2.5 months in 1810. If we're going to say that the Bonnie Blue Flag is the flag of the Republic of West Florida (and not a Confederate flag) because both are blue with a star we should also say that the Bonnie Blue Flag is the flag of Somalia.
If there is any doubt that the Bonnie Blue Flag is a Confederate flag, just look at the history of the CSA. When Mississippi seceded from the Union in January 1861 it was the Bonnie Blue that flew above the capitol dome. They didn't do that in reference to the Republic of West Florida, a republic that existed for 2.5 months over 50 years prior.
As far as compromise, no, we don't have to compromise on removing a Confederate flag as an official symbol of our state in the year 2020.