Jinnah (as in Mohammed Ali) was actually an abbreviation. I think his name was originally Jinnahbhai. Also I think it was of Persian origin, so not necessarily Muslim (could be Parsi). Other Jinnahs may be different.
While he was living here in Boston I was a close friend of HH Miangul Adnan Aurangzeb Crown Prince of Swat. His family knew Jinnah well and what he had said of him was that he was from a family of Moslems but was an Atheist. Prince Adnan studied Electronic Engineering incognito at Northeastern U. here in Boston then worked first for an engineering software firm. When that company moved to North Carolina he moved back to Islamabad. When the Bhuttos took power he then returned here where he next attempted to export ships to the breakers in Pakistan. He ended up as Assistant Manager of Tweeters Harvard Sq. selling Bang & Olufson to software and internet tycoons. He returned to Pakistan after the Bhuttos were out and entered politics rising to MP. I heard that there was recent a shakeup, he may have reentered International trade. If he ever move back to the States Tweeters has a standing job offer for him at HQ.