On the other hand, just because someone has a difficult experience it doesn't mean that on the whole the experience was detrimental. A lot depends on who the person is, what kind of help they have, and how they react to and integrate the experience.
This is much like reactions to difficult experiences in ordinary waking consciousness. One could go through an illness, for example, and come out of it stronger and with a greater value for the simple things in life you had taken for granted before. Or one could come out thinking "why me?", feeling sorry for yourself, feeling bitter at the world and life, or feeling persecuted.
In the MAPS therapeutic protocol that you mention (which is based on the work of Stanislav Grof), people are prepared for such difficult experiences, and if they happen are urged to stay with them instead of fightng them and trying to run away from them, to go deeper in to them, and afterwards are helped by trained therapists to deal with them integrate them.
All indications are that it is such an approach is what is responsible for the overwhelming positive outcomes of these studies, as opposed to the "acid casualties" that happen in informal, usually uninformed or even self-destructive casual use.