Juanita Brooks summarizes her conclusions from her 1950 study of the massacre.

Juanita Brooks

Juanita Brooks, The Mountain Meadows Massacre (Norman, OK: University of Oklahoma Press, 1950), 219–220

University of Oklahoma Press
Juanita Brooks, Brigham Young, George A. Smith, John D. Lee
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In summary, it seems that these are reasonable conclusions to be arrived at from the evidence at hand:

1. While Brigham Young and George A. Smith, the church authorities chiefly responsible, did not specifically order the massacre, they did preach sermons and set up social conditions which made it possible.

2. That this particular company met disaster was due to a most unhappy combination of circumstances: they were the first to pass when the war frenzy was at its height; their own attitude was such as to fan that frenzy and provoke added violence. Had they been of the temperament of the group immediately following, they would likely have escaped unharmed, although short of provisions and robbed of their cattle. But the reckless boasts and acts on the part of those who called themselves “Missouri Wildcats” culminated in disaster for the whole train.

3. While he did not order the massacre, and would have prevented it if he could, Brigham Young was accessory after the fact, in that he knew what had happened, and how and why it happened. Evidence of this is abundant and unmistakable, and from the most impeccable Mormon sources.

Knowing then, why did not President Young take action against these men? At the time, he was involved in a war and was too occupied and too far away to do anything about it. After he was relieved of his position as governor, he felt no responsibility, he claimed. He did have the men chiefly responsible released from their offices in the church following a private church investigation, but since he understood well that their acts had grown out of loyalty to him and his cause, he would not betray them into the hands of their common “enemy.” Perhaps the nameless “friend” who kept John D. Lee posted as to the movements of the government officials was not Brigham Young, but it could well have been. Someone assuredly warned all the participants, so that for many years they were all able to evade arrest.

4. The church leaders decided to sacrifice Lee only when they could see that it would be impossible to acquit him without assuming a part of the responsibility themselves. It was a case where the duties of a statesman were weighed against the loyalties of a personal friend, and the duties of the statesman, of necessity, were given precedence. To air the whole story would have done injury to the church, both among its own membership and in the eyes of the world, and this token sacrifice had to be made. Hence the farce which was the second trial of Lee. The leaders evidently felt that by placing all the responsibility squarely upon him, already doomed, they could lift the stigma from the church as a whole.

It was pressure from within the church, perhaps, as much as that from without, which demanded that Lee be convicted. He had never denied being present; he was known to have made the arrangements with the emigrants which decoyed them from their camp; and he had handled much of the booty. If by sacrificing one man the incident could be closed, why not co-operate to that end? “Better that one man should perish than a whole nation dwindle in unbelief,” was a quotation often applied to this case.

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