The assimilation process was more than just one planet whacking into another. It already began, ages ago - hence why Gaia appears to have two moons, one red and one blue. A scholar in Dagguero mentions this, and the fact that the moonlight doesn't seem to be reflected from Gaia, contrary to theory. The blue moon is Gaia's, the red moon is Terra's. The planets are merging on a metaphysical level, kind of fading into one. The Terran relicts, like those at Oelivert and Ipsen's castle, hint at the millennia-old process's history.

Kuja did destroy Bran Bal, and Garland, which probably interrupted the process somewhat. The idea was for the planets to merge, so that the Terrans ' souls could occupy the Genomes and live again, until they managed to wreck yet another planet. (Funny, we're never told how many planets have been assimilated throughout history, how big and deadly the Terrans have been.)

The IIfa Tree had a very violent reaction because the connection to Terra was severed. All of Gaia's souls could no longer be recycled into Mist, or siphoned off to Terra. The Tree responded by trying to kill what was threatening it. Kuja mentions this just before the battle with Deathguise.

At the end, we see the two moons merging. Perhaps they did, perhaps it's just symbolic of Terra and Gaia 'merging' in Zidane and Garnet, as others have suggested. However, I doubt the worlds themselves merged, and even if they did, the result would probably just be a bigger planet with additional landscape features, kind of like FFV Spoilerwhen the two halves of the world re-merge after the Void is unleashed.