Well they drew a lot from many religions, considering the concept of religion is a major theme in the show. I mean, let's consider the first main non-Mormon differences: they have a polytheistic belief system, and are monogamous.
They used obvious references from many religions for both of the show's main two religions. They did the same in Caprica as well. Not to say it was perfect... I simply don't think there was intent to proselytize the Mormon belief system.
The show's creator was a Mormon by the name of Glen Larson. Also according to Who's Who in America, Glen Larson is a member of the Mormon Church.
Battlestar Galactica was heavily based on similarities in plot with the Mormon Church and several of the church's doctrines were incorporated into the series. Mormon Expression did an entire very interesting podcast on the connection Battlestar Galactica has with Mormonism.
The Title Song/music says it all...