It took time for the church leaders to get the full story on what happened, but I don’t think they ever denied the massacre took place. The Church has expressed regret that it happened, but doesn’t accept any blame for it. What those men did there, they did in spite of being Mormons, not because of it.
Not so...
BECAUSE they were 'mormon', they were 'fearful' that this wagon train was out to get them!
Acting on those fears (generated in them BECAUSE they were Mormon), they lashed out and murdered.