I believe that the assimilation was stopped after the battles in Memoria......even if Kua had destroyed only Bran bal...or all of Terra....it wouldn't matter.....if you remember Garland mentions that the assimilation had already begun.....because he said that the mist was created as a by-product of Gaia's stagnating souls.....because the Iifa tree rerouted the Terran souls to replace Gaian souls......so when the group defeats Necron in Memoria.....(remember the FMV...Garnet and Zidane have to say goodbye to each other.....because he goes and save Kuja...his brother from the Iifa tree....and i believe that when the Iifa tree "freaked" out like it did.....it destroyed itself and stopped its mission which was never restored......Garland also mentions that the only way for Terra to fully assimilate Gaia is for all the Gaians to be destroyed because of war (hence Kuja and Zidane...his angels of death....chaos bringers).......Gaia still had plenty of living people still on it after the whole thing was said and done.....so i believe it was stopped.