Sorry, dangus, that's wrong. "Sanctae Romanae Ecclesiae" is genitive case. It's not the subject of (any) clause, but a possessive belonging to something else.
You could read it "In [the] extreme persecution of the Holy Roman Church, will sit Peter the Roman ..." or perhaps "In extreme persecution, will sit Peter the Roman of the Holy Roman Church ...".
For "Holy Roman Church" to be the subject of the clause, it would have to be "Sancta Romana Ecclesia".
Actually, the original text reads simply, “SRE.”