That is a very different thing than being a spy.
It is very possible that there are several such Indians who ply their businesses in Iran. Pakistan's ISI probably wanted to exploit one of these---it kidnapped Jadhav from Iran, and used his Muslim identity on his business passport to further the case that "if he had a fake passport, he must be a spy." If they have any evidence at all, why has it not been made available to various governments. For example, India provided not one, not two, but seven dossiers on Ajmal Kasab to various world governments before hanging him. And mind you, Kasab was seen by millions on video carrying AK-47s in Mumbai shooting. Still, we went through with full procedure.
Where is the evidence against Jadhav? Not one piece of evidence has been made public.