If we analyse the events,characters,their stand points and change of stance later, we can easily dig out the connection. Sir Sayed,the inspiration of the flag holders of Muslim League had said in TNT that Hindus and Muslims are two eyes of this country. During Khilafat, these two eyes started drifting apart and gave birth to a deformed face of divided India.There are several other factors,critical years like 1916,1928,1933,1939 and 1946 which need to be thoroughly studied. Then you will clearly understand the connection you are asking for.
Secondly,Nehru's idea of secularism was bound to face difficult challenges. What ever happened in Bombay with Khurshed Nariman and in Bihar with Dr.Sayed Mahmud during 1935 was a prelude to what was coming in the following years.But ideas flourish only after facing gruesome challenges and fortunately a large part of the Indian and Pakistani society still hopes to reverberate the ideologies dreamed by the respective founding fathers,no matter the appalling degree of criticism they face even after seventy years.