This is quite interesting. I myself know a few pilots of Indian origin, who definitely hold foreign passports and have been issued with Indian licenses.
Mercy 320, why dont you have the DGCA give you this reason in writing.
If memory serves me right, I do not recall remembering nationality to be a restriction for issuing Indian Licenses.
India is a member of the ICAO, and if other ICAO nations issue licenses to Indians, then DGCA must do the same.
Further, I do not see Indian nationality as a requirement for issue of a license in the Indian Aircraft Rules as specified here
http://dgca.nic.in/schedules/section-j.pdf good luck anyways!