Chinghiz Khan had already put in place the military organisation by the time of the Jin invasion. In 1205, when he became Chinghiz Khan, he had basically set up his affairs in order, and made full provision for succession in case of his own death (which he came close to, IOTL). And he had hugely competent generals - better military men than what Alexander had in his invasion. People like Jebei, Jelme, and Subotai are not going away anytime soon (unless the lost army included ALL these leaders). Any of them would pick up just where Chinghiz left off and would be back in a few years, after they had set right any disturbances in the wake of the Khan's death.