I must step in here to correct a misleading impression being conveyed here.
The problem between Sikh gurus and Mughal Empire was that of politics, not religion. It was seen as such by ordinary Muslims of the empire. For example look at the following from a Sikh religious source:
Gurdwara Katana Sahib, Gurdwara Alamgir, Gurdwara Phalahi Sahib, Gurdwara Raikot, Gurdwara Fatehgarh Sahib, India
"Gurdwara Ghani Khan Nabi Khan, Machhiwara, Dist. Ludhiana
Living in the town of Machhiwara were two Muslim Pathan brothers Ghani Khan and Nabi Khan who knew Guru Gobind Singh. It better times they had sold horses and received kindness from the Guru. Even at the prospect of facing certain death, the brothers agreed to help Guru Gobind Singh escape the surrounding area which was full of the Mughal army looking for the Guru. They had Guru Gobind Singh put on the blue robes of a Muslim saint and accompanied by his three Sikhs survivors of the battle of Chamkaur, they carried the Guru in a palanquin through the enemy lines. They were only stopped once by Muslim soldiers, but Ghani Khan and Nabi Khan were so convincing that the party was allowed to pass through enemy lines with their 'Muslim Saint' in disguise. This gurdwara honors the home of these two brave brothers."
The problems between Sikhs and Mughals started in time of Jahangir, when his rebel son received support from then presiding Sikh Guru in Lahore.
I have noticed that Hindus in particular like to fan the flames between Muslims and Sikhs. Pathetic.
In relation to the topic, I think that Sikhs made a mistake in the 1940s. Their presence would have been welcomed and would have made Pakistan a more inclusive country and society. Their mistake was our and their loss. Punjab would not have been divided, first between East and West Punjab, and then East Punjab into Himachal Pradesh, Haryana, and Punjab. Also, Kashmir would not have been a problem.