If FFIX's Online Ultimania was still up and running, I might be able to answer that question. As is, we don't know whether Kuja actually destroyed all of Terra or not, so there are a few scenarios.

1. Kuja did in fact destroy all of Terra. In this case, assimilation would stop because there was nothing left of Terra to assimilate into Gaia. The only thing that would be left behind would be the structures already assimilated into Gai.

2. Kuja only destroyed Bran Bal. In this case the assimilation of Terra and Gaia would continue despite the Iifa tree stopping and despite you beating Kuja. However, since the Iifa tree presumably stopped doing its function, the souls of the deceased Gaians would be able to travel back to the crystal according to the normal cycle of Gaian life.