You have to ask this point to Emperor Jahangir why he called him Isa Khan Afghan. However, he was the leader of all Afghan forces in Bengal who opposed Mughal domination.
We cannot just change history arbitrarily. Let it be what it is. We cannot revise it to say he was Isa Khan Rajput though he had a Rajput lineage from his father's side. Historical accounts call him a Khan and an Afghan because his mother belonged to an Afghan family in Bengal.
I understand you have a great love for history.
