I have to give Genghis some credit, if this dude was in my ethnic group I'd like him too. He kicked some serious ass. One of the best strategies of the Mongols was essentially tolerating the religions of the conquered. If they surrendered. By this single tactic he eviscerated the usual defensive strategy where the ruling class relied on religion to support the state. Once the religions realized they got to continue existing under the new regime, they were like fuck these guys and the Mongols got Fifth Column type support from the religions of the conquered.
And considering the fact that they were serious badasses, the other choice was have your entire country destroyed, get slaughtered and raped, and your cities burned to the ground. Compared to that, becoming part of the empire was a pretty enticing alternative.
It wasn't that vastly different than what the Romans did. As conquerors went, Romans were pretty good. The surrender condition was generally paying tribute, more or less getting to keep your original culture, and while you were paying tribute, anyone else who tried to attack you would get their shit fucked up.
And the alternative was the usual you all get killed and enslaved and your shit gets burned to the ground.
This was human culture for most of history.