To my knowledge it has only ever happened once in widely known recorded history, Maka. That was Carthage. What others are you thinking of? I suppose there is Ghenghis Khan but he only did it to particular cities rather than entire nations or civilisations.
Wiping people off the maps, pogroms, brutal oppression/suppression, those things are quite common. Rome had terrible problems with terrorists in it's outlying territories. They sent punishment armies to those regions to steal, rape, murder, and enslave as many people as they could find. Entire cities, villages, and ethnic groups were decimated. In recent times, Germany did this to Russia during WWII. No one really knows how many civilians died, but from the sources that are available from the Eastern Front tell us that the Germans were brutal beyond imagination. Thousands of villages were erased. Hundreds of small to medium cities were put to the torch. Dozens of large cities were completely razed to the ground. Leningrad was starved for 2.5 years to the point where the civilians at each other. If the Germans got a sniff of resistance in any of their newly occupied territory, they encircled a large geographic area and literally murdered everyone in it. In Russia, there are fields of bones as far as the eye can see from WWII. Scholars estimate that 40 million civilians or more died in Russia from the conquest.
So, this does happen all of the time, even in modern times. Anyone who resists the Empire is usually put to the sword.
The exception, IMO, is Britain and the US. Britain has had it's share of people it's wiped out in it's various colonies, but it seemed like that imperial power would rather rule through proxies and have others do it's dirty work. The US picked up the same system after WWII, neatly stepping into the power vacuum hen Britain gave up the Empire. In some ways, the British Empire never went anywhere. Think of all the prominent American politicians who are inducted into Knightly orders and pledge to serve the Queen. President Reagan, President Bush, and many key placed underlings belong to these Orders. Even if it all is just ceremonial, does it really matter if the empire is being maintained by US power?
The "special" relationship between Britain and the US is fascinating. The impression the world gets is that Britain follows the US, but what if, in the level of power above national governments, it's the other way around? There is a reason why the financial center for the entire world is located in the City of London, for example.
Anyway, I'm just musing now. The point here is that Empires have always engaged in mass murder, especially when the conquered people resist in any way. This doesn't stop the resistance, even Ghengis Khan, who razed entire cities to the ground, engaged in mass rapes and murders of millions, and would literally build mountains of skulls, could not quench the human spirit for vengeance. Famously, Ghengis would murder any child higher than a wagon wheel because he knew that this child would be young enough to forget what happened to his family and would not seek vengeance.
This is how I know there is no hope to solve this problem with violence. There is no proxy ruler big enough, mean enough, or brutal enough to ever squash these people into submission. The best, cheapest, and most peaceful thing the government could do is walk away. Let the people develop their own economies, cultures, and social institutions. The extremism will disappear exactly as it has in the West.
Of course, for this to happen, the people in the West will have to understand just how far divorced the State has become from their interests. The Empire does not benefit us at all. Not like Rome. We don't get slaves or gold shipped home to serve the cities. We get propaganda and we get to fight and die and we get to pay with our unborn childrens wealth. Every time I see stories like the one above, this big picture is plastered on it. Most people have red propaganda glasses strapped on by the State, so they can't see the bloody pattern.