Even the Mongols, who killed over thirty million people in their conquests and were some of the most bloodthirsty invaders on record found it more worthwhile to set themselves up as leaders. Why would they make China a desert when they could make the Chinese build them a pleasure dome?
Invasions occur in search of resources. Land is only one particular resource. People are by far the most useful resource for any ruler. Natural resources without people are useless. Consider that the Roman empire, one of the most successful conquering people, built its power not on the land that it took, but on the people it took. Killing a population upon conquest would be like dumping all the captured gold into the sea. If, say, the Romans had wiped out every person in Gaul, it would have not made them more safe. It would have made them less safe, because they wouldn't have had the people to occupy it and the vacuum would have been damn attractive to all those Germans over the Rhine. Better to create a nice, assimilated Romanized Gaulish population as a buffer between those nasty Germans and Italy.
Keep in mind that the nationalist revolts of the 19th century were the result of an entirely new way of viewing the world. Before than, nationalist revolts were relatively rare. If you look at the history of the great conquering peoples (Macedonian Greeks, Romans, Mongols, etc.) you see little if any "nationalist" revolts against their rule. For most of the common people in those eras, it was just new boss, same as the old boss. Why should they care if their masters spoke German or French? They still owed the rent.