In Ghengis Khan and the Making of the Modern World, Jack Weatherford compared Mongol brutality under Ghengis Khan to that of some contemporary civilizations. His treatment comes out as pretty sympathetic to the Mongols, despite acknowledging some the atrocities they committed (e.g.: the extermination of the residents of Nishapur).

Weatherford makes two main arguments. First, that Ghenghis Khan waged war with an overriding strategic imperative of preserving Mongol life.

Unlike other general sand emperors in history who easily ordered hundreds of thousands of soldiers to their death, Genghis Khan would never willingly sacrifice a single one. The most important rules that he created for his army concerned the loss of soldiers.

To the extent that non-Mongol civilian populations could be used to further this goal, the Mongols treated such populations differently (although not much better) than traditional armies at the time.

Traditional armies of the era treated villages as resources to be looted and the peasants as a nuisance to be raped, killed, or disposed of in any convenient way. By contrast, the Mongols, who were always low in numbers compared with the place they invaded, put the massive number of people to strategic uses.

In his campaign against the Jurchens, for example, Ghengis Khan's armies herded up peasants like cattle in front of them to sow confusion, and to serve as shields and as "living battering rams." (Weatherford, p.91-92).

Second, Weatherford argues that although the Mongols were ruthless and efficient in killing their enemies, and in this way inspired terror, they were less likely than others at the time to use torture or mutilation to achieve this purpose.

By comparison with the terrifying acts of civilized armies of the era, the Mongols did not inspire fear by ferocity or cruelty of their acts so much as by the speed and efficiency with which they conquered and their seemingly total disdain for the lives of the rich and powerful. The Mongols unleashed terror as they rode east, but their campaign was more noteworthy for its unprecedented military success against powerful armies and seemingly impregnable cities than for its bloodlust or ostentatious use of public cruelty.

(Weatherford, p.115-119).

If you're interested, I highly recommend the original source. The relevant pages are p.91-91 and p.115-119, which are available here in pdf form.