Here are some important quotes:
"Leonard J. Arrington, founder of the Mormon History Association, reports that Brigham Young received the rider, James Haslam, at his office on the same day. When he learned what was contemplated by the militia leaders in Parowan and Cedar City, he sent back a letter stating the Baker-Fancher party were not to be meddled with, and should be allowed to go in peace (although he acknowledged the Native Americans would likely "do as they pleased").[11][16] Young's letter arrived two days too late, on September 13, 1857.
Part of the article also stats that the main instigators not only were kicked out of the church, but were also put on trial.
Context is important in all things. For example:
"In addition, during the prior decades, the religion had undergone a period of intense persecution in the American Midwest, and faithful Mormons moved west to escape persecution in midwestern towns. In particular, they were officially expelled from the state of Missouri during the 1838 Mormon War, during which prominent Mormon apostle David W. Patten was killed in battle. After Mormons moved to Nauvoo, Illinois, the religion's founder Joseph Smith, Jr. and his brother Hyrum Smith were assassinated in 1844. Just months before the Mountain Meadows massacre, Mormons received word that yet another apostle had been killed: in April 1857, apostle Parley P. Pratt was shot in Arkansas by Hector McLean, the estranged husband of one of Pratt's plural wives, Eleanor McLean Pratt.[45] Mormon leaders immediately proclaimed Pratt as another martyr,[46] and many Mormons held the people of Arkansas responsible.[47]"
So after being kicked all over the country and having many loved ones killed, and misconstruing the emigrants as part of the mob that killed yet another leader of the church, the people apart of the Mountain Meadows Massacre decided not to take it anymore. Obviously it was a massive mistake, but context makes it understandable. This was, after all, the wild west we're talking about here.