Anyone who has been following this story closely will know that there has been a lot of tension between Duterte and the Church on this issue (and others) since even before he was elected president.
I suspect that waiting to openly confront Duterte was a pragmatic decision (as in, 'maybe we can talk him out of it in private first'). People make it sound like the bishops were just sitting around while individual priests and nuns worked against this to help people. I would not be surprised at all if those religious were acting with the support of their bishops.
Going by the Catholic Church's track record (like thinking Franco was the greatest), it's safe to say this has more to do with his expansion of birth control, pro-gay marriage stance and staunch anti-Catholicism than the actually terrible things he's doing.
BRTD, I'd like to know, since you consistently point out his positions on those issues, do you see Duterte as an opportunity to liberalize the Philippines?
I really hope you're not taking the attitude of 'at least he's good on that stuff,' because that is exactly the kind of sickening mentality that led (in the opposite direction) to Catholic support of fascism and dictatorship in Latin America and elsewhere.