Roman Catholicism (and at least some other "high" churches, like the "Eastern" Orthodox) has a doctrine that is little known among outsiders. While these churches do stress obedience to the hierarchy and impose sanctions for disobedience to the hierarchy, they also admit that individual conscience can validly (if not always "licitly", to use a term of the Latins) lead someone to act in disagreement with the hierarchy. However, one must be careful that one is actually acting from conscience and not merely rationalizing. In addition, if the hierarchy imposes sanctions, one needs to remember that they are also likely to be acting in good conscience, perhaps on incomplete or erroneous information, but still in good conscience. There is a doctrine known as "invincible ignorance", which is also little-known among many Protestant and allied groups. That is to say, it is possible to be wrong without being damned for it. Thus, someone could be "excommuncted" or "anathemized" and still saved, depending on that person's individual circumstances. Excommunication is the term favored by the Latins, as befits their generally legalistic approach. The East, on the other hand, prefers "anathemized", which is the term actually used by the early Church. "Anathema" literally means "offered over" or "offered up". That is, the Church says "We can't deal with you, so we're leaving you to God to do with as He pleases (but we think He won't like you, either)." However, in the old Tradition, the Church does not arrogate the privilege to actually pronounce damnation on its own authority.
That being said, many modern Christians interprete "excommunicate" or "anathemize" as being consigned to hell on the authority claimed by a Church.
In short, yes, Rome may pronounce against Freemasonry, but there is still a safety valve, and hierarchs will argue vehemently against that valve. Doesn't make it any easier for Roman Catholics when rubber meets the road.