I was curious about that myself. I contacted Joan at the Clan MacKinnon Society of North America to find out. It has nothing to do with Mac being protestant or Mc being Catholics. That is what my family believed. Some think it's Mac for Irish and Mc for Scottish. Wrong again. Since our progenitor was born in Scotland, it pretty much kills that theory also. In some family, you will have some generation spelling MacKinnon and the next McKinnon. So what this all mean is, it was a personal choice. They may have created their own reason, but none of them are actual fact.
Joan also related to me a story about one of her aunts that spelled the name M@Kinnon, in other words, she wrapped the c around the a. So this could have been missread and looked more like McKinnon. That is the explanation that was given to me.
Hope this answers your question.