It is true that Islam was not having cast system in India. But there were divides from day one like Sunni/Shia. Later own Ahmediya and Dawoodi Bohras were emerged as seperate communities or casts.
Sunnis also have two main categories. Wahabi(in India/Pak Deobandi) and Sufi. The Sufi think thank diluted the South Asian and upto some extend the Persian Muslims from the fundamental Islam which is original one as per Quran and Hadiths and followed by the Wahaabis.
This so called Sufi influence made South Asian Muslims more tolerent towards the the Kaffirs at least allowing them to exist unlike what happened to Jews, Paagans, Parsis and Christians of Arabia in hands of their wahabi counter parts.