Although women heads of state are not so rare in democracies nowdays, in the 60's they were the exception. And even today India makes the headlines with religious norms conflicting with women's rights.
So was Indira Ghandi's gender an issue during her term as prime minister? And did her time in political office signify any shift in gender relations in India?
To start out with, the question is I am afraid vague.
Women's rights has been enshrined in the Indian constitution since 1947 and the majority Hindu religion has no religious norms that conflict with Womens rights. Yes, some regions have cultural practices that do affect women's rights but these are in pockets and not widespread. So I would request you to please clarify on just exactly what this conflict it is that you are speaking with.
If you go back to the period from 1875 on, Women have been at the forefront of the Freedom movement, the likes Annie Beasant (a British socialist who was the vanguard of the nascent Indian freedom movement lead by civil society), Madame Cama, Kamala Nehru, Vijayalakshmi Pandit, Sucheta Kriplani, Durgabai Deshmukh, Anasuya Sarabhai, Lakshmi Sahagal and a whole host of others too numerous to name individually. They were independently recognised, many were powerful orators and were accepted as leaders by the masses.
Go back earlier, the period 1650-1875 and women Queens and rulers abound, Rani Lakshmibhai, Ahilyabhai Holkar, Rani Tarabhai (she all but ran the powerful Maratha Empire after the death of her spouse), Jijibhai Bhosale, Chennamma, Avantibhai, Velu Nacchiyar and again, too many to list.
These were not accidental rulers, but trained in the ways of warfare, and highly educated, they took power in their own right and were accepted by their subjects.
We could go even further back in time and I could list many more such examples of Women rulers and leaders.
The point being, India and Indians as a culture was used to and still is used to seeing women in positions of power.
To answer your specific question though, Indira was identified as a figure head and a possible puppet by a group called "The Syndicate", but she out played them and split the Indian National Congress, stood for elections on her own, and defeated the syndicate. To the public though, she was very well received and was very popular in her own right. Even opposition leaders like Vajpayee likened her to the powerful Shakthi goddesss, Durga.
I am afraid I am not sourcing this argument as I have covered a vast period of almost 350 years, and your question is like I said vague. If you would like me to source any particular period or person, do let me know and I am happy to do that.