Haha, Trance Kuja can't destroy towns in one go but we saw the vastly weaker Odin doing so. Heck, Atomos could have eaten all of Lindblum if Lindblum hadn't surrendered.
And UK is right - Kuja did transport Zidane and them away from Necron at the end of the game. As for why he didn't teleport them away when he fought them at the Crystal, who knows. He probably underestimated them or he just figured they'd all be killed by either him or the Iifa Tree so he didn't bother.