The had part for Christians would be the foundational belief that Jesus is the only way to God and salvation and that he came and died for all humanity. How could Jesus sacrifice himself for people on another planet who had no possibility of knowing what he did for them?
Well, neither did the Aztecs or the aboriginal Australians, but that didn't shock the foundation of Christianity. The "good news" (to borrow a Christian term) did reach them when time was due. I would think that the same would apply to alien life forms.
And about the fact that the Colonials are polytheistic, well, I suppose that they would deal with it like they do now with people of different religion (or no religion). A lot of Bible thumping and bell ringing at Sunday morning.