This question of conspiracies and Mormons in regards to Twain prompted 
some additional reading for me.  I doubt that the Mormons were of much 
significance to Twain as I suspect his Mormon Bible chapter was little 
more than  fill - as he was known to do throughout his career.  The 
Mormons were nothing more than another characteristic of Washoe for him.

It appears he was aware of the so-called Mormon question before arriving 
there and that his primary awareness of them was their practice of 
polygamy.  He knew of the Mountain Meadows Massacre but it wasn't until 
several years later that he accepted the idea that the Mormons were 
responsible.  I'm sure he thought the Indians had done it.  It's likely 
that Mrs. Waite’s book, “The Mormon Prophet,” convinced him otherwise.

"I left Great Salt Lake a good deal confused as to what state of things 
existed there—and sometimes even questioning in my own mind whether a 
state of things existed there at all or not. But presently I remembered 
with a lightening sense of relief that we had learned two or three 
trivial things there which we could be certain of; and so the two days 
were not wholly lost. For instance, we had learned that we were at last 
in a pioneer land, in absolute and tangible reality."