Well, the material grounds for the excommunication were faulty. Cushing and Father Feeney's Jesuit superiors were manifest heretics and had therefore ipso facto vacated their offices, and so there wasn't anyone for Father Feeney to be disobedient to.
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You are presuming Feeney is correct. But he is not correct. The idea of baptism of desire by implicit faith was taught by numerous theologians and none of them had been condemned. So Feeney does not have the authority to condemn a doctrine just because he disagrees with it.
Those days were very different from today inasmuch as there was a true pope who condemned error, so it's easy for people now to think theologians were all just writing heresy back then, but that is an anachronistic idea. In the time of Leonard Feeney, theologians were not permitted to write heresy, so Feeney's accusations of heresy were incorrect. And since they were incorrect, he still had a superior whom he disobeyed.
Let's leave the theology aside for a second and just look at this situation from a common sense point of view for a second. Does it really make sense that all these theologians were teaching heresy during the reign of an unquestionably true pope, and only one priest in the world happened to notice this? Really?
Even if you believe it was legit (it was not, as his only crime was teaching EENS dogma while those around him denied it)
I have said consistently that Feeney was excommunicated for disobedience. It's the Feeneyites who want to say he was excommunicated for his teaching, in order to make him into some sort of doctrinal hero.
Feeney was excommunicated for a protracted period of disobedience to his religious superiors, finally including the most sacred tribunal in the world, the Holy Office, who ordered him to come to Rome, whom he disobeyed.
It's obvious to me, from reading "The Loyolas and the Cabots", that for Feeney it was never about doctrine anyway. It was about having a creepy personality cult of people who worshiped him to the point where they refused to ever receive the sacraments from any other priest. He just used this supposed heresy as a tool for controlling those people who followed him, as a way of telling them he was the only priest they could ever get the sacraments from. This was clear from the beginning of the book. When he was first ordered to leave that place, that woman who ran it went in to the bishop and said they didn't want Feeney to leave. The bishop told her she should be willing to accept the ministrations of any priest, a most correct and Catholic principle. She responded that she refused to accept any priest who didn't teach them the same ideas as Feeney did. See? The goal was control all along.
This is made even more obvious when he was asked to go to Rome. If the purity of Catholic doctrine and the salvation of souls had been his goal all along, he would have jumped at the chance to go to Rome and report on the people who were causing so much scandal in America. But no, doctrine was never the goal. By that point he already had his weird little group of people who worshiped him, so he didn't need anything else after that, which is why he round-filed all the subsequent mail he got from his Jesuit superiors, the diocese of Boston, and even the Supreme Sacred Congregation of the Roman and Universal Inquisition, which is its real name. The most sacred congregation on earth, operated directly by Christ's vicar. He continued to offer Mass and administer the sacraments even after his suspension and excommunication, which was sacrilegious.
Shame on that evil, wretched man.