It has been hinted since Marineford that the CDs will fall hard at the final war, but I don't think they'll be brutally annihilated. Villains in One Piece, especially the worst ones, usually don't get 10% of the suffering they caused. The only ones who faced dire consequences were Kaido, Big Mom (these two could still be alive though), Orochi, Arlong, DoFlamingo and, last but not least, Hody (btw, this is one had the hardest fall).
Buggy is a Yonko currently (and Alvida's with him). Kuro and Krieg survived their encounter with Luffy (Fullbody and Jango even became marine officers at the HQ, although Gin, who was more honorable, possibly died of Krieg's poisoning). Croc slipped away from Impel Down and now is better than ever. Enel achieved his dream. Spandam and Lucci got promoted to CP-0. Moria had some tough times, but is still active (probably fled from Hachinosu). Charlos was battered two times, but in the end one of his opposers was executed. Caesar managed to get out of the clutches of two Yonko and reunited with Judge. Doffy may even be rescued from Impel Down by Cross Guild (or he himself could escape, Pica and Señor Pink are tailor-made for that).
Oda likes to redeem villains. It even happened once with one of the CDs (Mjosgard).