"Only the Roman Church" would be "Sola Ecclesia Romana", since adjectives must agree with their referents in number, case, and gender. "Only the Church of Rome" would be "Sola Ecclesia Romae" (Romae = genitive form of "Roma").
Thus endeth the Latin lesson for today. We now return you to our regularly scheduled program, "the fictional Protestant history of Scottish Christianity".
Oh, my. I just had flashbacks to Mrs. Bailey's 9th grade Latin class.....