I think it's pretty clear that even if it wasn't intended to prohibit telling civil authorities, that is still how it was interpreted and enforced, otherwise we'd see a higher report rate tham the 24% (i'll re-edit with citation) we see in america (and significantly lower in ireland i'd bet)
possible, though I think most of the cases that make it into the press currently are from well before 2001 (when the Vatican pulled these cases to Rome) and that prior to that it was local clergy that dealt with the cases as they saw fit - and that one of the problems in the Church was and probably still is not so much that they encourage covering things up directly but that the local clergy doesn't have any incentive to aggressively report suspicions and may even have had or still have the impression that a large number of reports (both to civil authorities and to Rome) indicates that someone locally has lost control and should be replaced. But that is just my interpretation. I'd also like to know how many cases actually happened after 2001 or whether there is indication of coverups after that, as well as how if at all reporting has changed. Though its hard to judge since report rates are notoriously hard to quantify.
Edit: as for keeping clergy in the ranks: it has no direct connection to alleged coverups and as far as I understand the Catholic Church local Bishops have very wide latitude in keeping clergy from work in congregations - so that I do not think that please from the US to defrock certain clergy had much of an impact on actual cases - mostly because they could and I would hope did remove these priests from any work involving vulnerable congregants. It does obviously pose other questions, such as whether it was advisable to keep them around as priests for so long for publicity reasons and to show internally that such behavior was not sanctioned by the higher ups - but not so much about whether the Vatican was responsible for allowing them to continue their abusive acts. Of course I could be much mistaken - but at least with the German system I am quite certain that how and where and whether any priest is put to work is almost entirely up to the local Bishop and not up to Rome.
Now of course with me not being part of the Catholic Church my views are mostly informed by published writings and not direct knowledge
