I have three ideas:
-- Make it so that when people leave the planet they revert back to their natural state. Meaning that if the Baku are taken off the planet most of them will rapidly age and die.
-- Reverse the origins of the Baku and the Sona: make it so that the Baku are actually an offshoot of the Sona rather than the other way around. And also make it explicit that the Sona have been infected with a genetic disease which makes them sterile (this is only implied in the actual film).
-- Release the movie in 1999. After the end of the Dominion War. So no one will be complaining about it having nothing to do with the Dominion War.