India and Pakistan were formed under a two nation theory championed by founder of Pakistan M.A Jinnah. According to it Muslims were different people from Hindus and hence two could not exist together. His main worry was that caste Hindus would dominate an independent India and hence muslims needed a country of their own. So, in a sense it was more Muslims spinning off and forming their own country rather than an equal division. In such a scenario every community except Muslims were to be in the state of India. Off course Nehru and Gandhi decided that any Muslim who wished so can stay in India and will have same status as anyone else. States with Muslim majority went to Pakistan and those with Hindu majority to India. Unfortunately for Sikhs, punjab was one of the two states that was to be divided between India and Pakistan.

There was no official migration of people. People could chose if they so wished. The migration that actually took place was mainly due to the communal violence. Sikhs had very little choice in choosing India. When they started getting killed in Pakistan-Punjab, they had no option but to migrate to India. I can't comment on Sikhism being similar to Hinduism but Hindus don't consider Sikhism alien. It is same in the case of Buddhism and Jainism and might have to do with their Indian origins. Due to this there was very less danger to Sikhs from Hindus in India as compared to Muslims in Pakistan.

Follow-up question: was it seriously considered by any officials during the partition to have an independant Khalistan for the Sikhs?