Well based on the available sources we have no idea if this actually happened. The two sources which are used to claim that Genghis Khan's funeral saw the mass slaughter of those at the burial sight or even everyone along the route his corpse was transported down is based on two major authors Rashid al-Din and Marco Polo. While the eminence of these writers means that many have accepted their claims they are far from unproblematic. Rashid-al Din was writing some 50 years after the event and would be reliant on hearsay being unable to speak or read Mongolian himself. Meanwhile Marco Polo does not makes this claim specifically about Genghis Khan and instead claims it to be a funeral custom for all Mongol rulers, and mentions it in an account of Mongke's funeral. He would not have witnessed this either arriving some 14 years after the event.

While this does not mean that we should dismiss their claims out of hand the lack of mention of these practices by other sources makes them dubious. The fact that no Chinese or Mongol source makes any mention of this is pretty notable. The Mongols had little problem in describing their own extreme violence (see The Secret History of the Mongols) and many Chinese writers got a lot of mileage writing about Mongol brutality, even under Mongol rule. Equally papal envoys like William of Rubruck and Plano de Caprini who, unsurprisingly, were interested in Mongol religious and cultural practices make no mention of such rituals.

Off topic : can you link where you saw this?