Is she still associated with the radically left, anti-Israel and pro-partial birth abortion Presbyterian Church of USA? It appears that she was as of November 16, 2004. That won't sit well with many social conservatives.
http://www.layman.org/layman/news/2004-news/bypassed-for-pcusa-honors.htm
George and Laura Bush are associated with the United Methodist Church. Hasn't hurt them a bit. You can vote for some fringe candidate if you like, but you won't have a lot of company.
I think you'll find that the Church has left Condi and her family, even though they have not left their Church.