First off, the CDF does NOT go hunting for errant priests. They don't have the resources. Something is brought to their attention first, it is investigated, THEN an action or actions are taken. It was even referenced in the third to last paragraph of this article. You just gave the Libs a red herring.

As to the silence of the Pope, does he condone what Flannery, D'Arcy, et al advocate is does he reject it? The silence appears to be a cowardly move on the part of the pontiff.

Has Flannery, in essence, self excommunicated? The order was not vacated by any silence. 

Let us pray for his repentance.