First of all, the word "final," in relationship to the persecution of the "Holy Roman Church," puzzles me. The HRC is, by far, the largest religion in the world, and if anything, it is known for persecuting others! I wonder if that is what Malachy meant; that it would be the HRC which would be the one doing the persecuting? In Revelation 13:11-18, a religious leader, known as "another beast" (v. 11), is also known as the False Prophet (Rev. 16:13; 19:20; 20:10). He will create an idol, a robot-like image of the Antichrist, and demand the whole world worship it (Rev. 13:14-15). Yes, during the Tribulation, it will be the religious leader who will do the persecuting!
Secondly, notice the prophecy says he will "pasture his sheep." These followers are not the Lord's sheep/flock, but are HIS! When Jesus "commissioned" the "original Peter of Rome," He told Peter three times to feed "My sheep" (Jn. 21:15-17)!
Thirdly, while the true Church is known as the pure Bride of Christ, the whore who sits on the backs of seven mountains, or world empires, is described by John: "And the woman which thou sawest is that great city, which reigneth over the kings of the earth" (Rev. 17:1-18). When John wrote Revelation, "that great city which reigneth over the kings of the earth," was Rome!
Fourthly, the true Church will not be present on earth during the Tribulation (Rev. 3:7-11), and the only church present, the one the last Pope will "pasture," will be the Church of Laodicea, a church void of the presence of Jesus Christ (Rev. 3:14-20). Since the Tribulation ends with the return of Jesus, who will judge the nations (Mt. 25:31-46), why would the Pope's church view Him as "the dreadful judge?" The true Church rejoices at the return of the Lord, while the church to which the Pope tends, sees Him as one of whom they should dread His coming!
There is irony in the teaching of the HRC, that in order to be saved, one must be a faithful, practicing member of the Pope's church. The exact opposite is true; Paul wrote that any church which teaches another Gospel, a Gospel of works, should be cursed (Gal. 1:6-9). He also wrote to come out of such a church (2 Cor. 6:14-18). Salvation is a free gift, provided and offered by God to all who will accept Jesus by faith (Eph. 2:8-9)!
Following Christ leads to joy! Following the Pope leads to dread!