I personally do not see the brutalities of any empire from the last one thousand years to be acceptable, people were civilised enough by 1000 AD to know right from wrong. Alexander, Caesar, etc lived in a time where people lacked a solid set of morals, and thus had no reason to believe that anything they are doing is wrong. The Ottoman Empire on the other hand were officially Islamic, and even held the title caliphate. Despite having a set of morals to follow in the shape of Islam, they went on to use Islam for legitimacy, bend the rules, and commit the same brutalities as people committed in pagan times.
Also, many of the brutalities carried out by the Ottoman Empire happened in the last couple of centuries. Between 1913 and 1923, the Ottomans committed a genocide of Christians, including around 1.5 million Armenians, 200,000 Assyrians, and 500,000 Greeks, the effects of which are still lasting today. I see almost no justification. The Ottomans, and Turks in general, have overall done very little good for this world. Their empire was regressive, and they are almost solely responsible for the decline of Middle Eastern Civilisation, and Europe eventually overtaking in fields of education, philosophy, culture, and science.