I'm not sure we can/should assume a lack of
animosity. In most cases, these things exist alongside animosity. Human culture is very complex and the story is usually multifaceted.
We all recently revolted against the last empires and quasi-empires in favour of nationalism. It's hard to say it was unjustified, and it often came with democracy and other aspects of liberty and liberalism. But empires have played complex roles in human history. They were oppressors and enslavers, but also collectors of culture and scholarship. Enablers of travel, commerce and cultural exchange. They brought disparate cultures together, voluntarily and involuntary.
Massive empire building in many cases left culturally rich legacies. The Mongolian empire opened east-west exchange of ideas and contact between scholarly, religious and artistic culture throughout all Eurasia. Some credit it with enabling cultural movements like the Italian Renaissance. This was alongside atrocities. Look up the conquest of Baghdad.
The Baghdadi Jews the article references have a long history with empires. The community started 2700 years ago, when the King of babylon conquered Judea and shipped Jerusalem's elite to the Bagdad area. The enormous Persian empire conquered Babylon and they were at the center of a cultural superpower. Then Alexander's Greeks Came, then Romans, Parthians, Caliphs, Khans, Seljuks, Ottomans... Many Emperors. Much blood. Much art.