You should check out the work of Ehud Toledano for a set of well researched works regarding slavery in the late Ottoman Empire.

"How brutal" is a difficult question to ask because "brutal" is vague and not well defined. Even with a bit more qualification assessing relative brutality would be a dicey issue, as any slavery by its nature is a brutal institution.

What I can say is that, is that slavery in the Ottoman Empire had some differences from that of Christian Europeans or Americans. Slaves from Africa were typically brought over the Sahara to North Africa, or across the Red Sea to the Hejaz, to serve as eunuchs for the households of notables. Use of African slaves for agriculture, which was the main use of these slaves in the Americas or Caribbean, was not common. Mehmet Ali Pasha of Egypt tried to institute a slave army of Sudanese, and even attempted to build some plantations using black slaves as agricultural labor along the lines of European slavery, but failed.

Household slavery in Islam is a difficult concept to understand because we are so familiar with large scale plantation-agricultural slavery in the Americas. Eunuchs would be purchased in order for them to join a household to protect and serve the women and children. Ottoman notable households would try and model themselves on the Imperial household in Istanbul, which employed a large amount of slave eunuchs until the very end of the empire, long after slavery was successfully suppressed in most the empire. These eunuchs could gain a large amount of influence in the imperial household.

The relative influence and comfort that a slave eunuch could attain as part of a wealthy Islamic household needs to be understood in the light of the great violence that was necessary to seize a human, impress them into slavery, mutilate their body, and transport across great and inhospitable distances to the population centers of the Islamic world. According to Toledano, due to a lack of reliable sources it is nearly impossible to assess mortality rates of humans being mutilated in such a way as to create eunuchs, but as this was being done in the era before modern medicine, it must have been quite high.

TL;DR The Muslim slave trade that brought Sub-Saharan Africans from Africa to major Islamic population centers was brutal, but different from the more familiar European and American context.

Very strange, such a important historical topic and no one can suggest a good academic book about it? =(

Perhaps a clarification by the question writer: Do you mean treatment of the slaves in general, or just during the period that they are being "traded," i.e. moved from place to place with the intent of selling them at the end of the journey?

I ask because Linda Colley's Captives: Britain, Empire, and the World, 1600-1850 discusses the differences between how British people taken into captivity in North Africa differed from southern and central Africans taken to the New World, but the British in North Africa were generally taken on the high seas in the Mediterranean and thus had relatively short voyages to their points of sale. But the treatment of African captives taken north for sale is beyond the scope of her book.

I only know of a small part of the arab slave trade, as in its relation to the naval wars of the 16th and 17th centuries.

Roger Crowley covers some of the slave trade in his book Empires at Sea. Venice, Spain, the Papal State, and Genoa each spent much of the 16th century fighting the Ottomans for control of the Mediterranean, and the ships they used were manned by oarmen. It was not fun being an oarman, you were there entirely as an engine for a boat/weapon, and you had a very short life expectancy.

In the battle of Lepanto alone, nearly 30,000 people lost their lives. The Christian side was oared by convicts and slaves stolen from the North African coast; the Muslim/Ottoman side was oared by Christian slaves stolen from the northern coast of the Mediterranean.

Some famous pirates you might have heard of such as Barbarossa and his brother Oruç got their naval beginnings working as corsairs raiding christian settlements for captives to sell in to slavery (generally to oar the fleets of the Ottomans).

Roger Crowleys books are all very good, highly recommend them if you are interested in this time period.