Every villian/maniac had faced certain experiences in his past life which had made him do things he did.. be it terrorist/suicide bombers or the cruel invanders.
In the series, Babur is the main protagonist of the story, and they totally skip the details of post-war horrors - how innocent natives of that land are killed/raped, most importantly when the invaders belong to a different religion from a far fetched land. They do not consider other as another as human being - and every heinous act is justified.
In general also, fighters are trained to hate their enemy - which makes them fight more effectively - for Mughals - it was in name of their religion.