The reasons Sikhs are seeking Khalistan are the same reasons due to which we sought Pakistan. They just want the space and security to run their affairs themselves, have a Sikh law board and work to improve things for people of their religion. Pakistanis generally do not support them because they are only Sikhs. Well muslims wanted the same thing when we formed Pakistan and we got it.
I believe Sikhs should have vouched for Pakistan, especially the offer Jinnah made. They could have formed 15% of the population of Pakistan and would be a much more influential minority. I feel if we had more minorities we would benefit too as it could be a counter balance against terrorism and minorities always have had a role in reducing terrorism. Sindh still suffers far less terrorist violence. 20% Sindhis are hindus and they have no Islamic religious extremism. Bengalis have 15% Hindus in their nation and don't have a terrorism problem. If God had intended us all to be muslims he would have made each race, each nation muslim. It is because Allah wants us to learn from others that there are minorities too amongst us.
Sikhs made the right decision not vouching for Jinnah. They'd have been wiped out by now if they'd gone to Pakistan instead staying with India. We're not exactly role models when it comes to treatment of minorities. But the one thing that we can say with absolute certainty is that we do a better job than Pakistan.