That's why these successful programs are always therapy-first, rather than drug-first. The focus is first on identifying and fixing problems, using drugs to potentially amplify the therapy rather than avoid the problems.
Sadly, most of these studies lack any control groups (e.g. therapy-only) to compare against. If you look at the graphs in the study, patients were already reporting massive improvements after the first 3 therapy sessions, before taking any MDMA at all. Unfortunately, I don't think we can draw any conclusions about the MDMA in this study other than it didn't appear to make things worse when it was introduced.