"Concerning the separation of the Presbyterian Church from Rome, Dr. Guthrie writes: “Three hundred years ago, our church, with an open Bible on her banner, and this motto, ‘Search the Scriptures,’ on her scroll, marched out from the gates of Rome.” Then he asks the significant question: “Did they come clean out of Babylon?”—Thomas Guthrie, The Gospel in Ezekiel, page 237. GC 384.3"
"And I heard another voice from heaven, saying, Come out of her, my people, that ye be not partakers of her sins, and that ye receive not of her plagues."
The EGW passage, while quoting Dr. Guthrie, implicitly connects the call to 'come out of Babylon' (Revelation 18:4) with the separation of the Presbyterian Church from Rome. The question 'Did they come clean out of Babylon?' directly alludes to the verse and its meaning.
"“The Church of England,” says Spurgeon, “seems to be eaten through and through with sacramentarianism; but nonconformity appears to be almost as badly riddled with philosophical infidelity. Those of whom we thought better things are turning aside one by one from the fundamentals of the faith. Through and through, I believe, the very heart of England is honeycombed with a damnable infidelity which dares still go into the pulpit and call itself Christian.” GC 384.4"
"For the time will come when they will not endure sound doctrine; but after their own lusts shall they heap to themselves teachers, having itching ears;"
The EGW passage, quoting Spurgeon, describes a situation where people are turning away from sound doctrine, which aligns with the warning in 2 Timothy 4:3 about people not enduring sound doctrine and seeking teachers who cater to their desires. Both passages address the issue of apostasy and the rejection of truth.
What was the origin of the great apostasy? How did the church first depart from the simplicity of the gospel? By conforming to the practices of paganism, to facilitate the acceptance of Christianity by the heathen. The apostle Paul declared, even in his day, “The mystery of iniquity doth already work.” 2 Thessalonians 2:7 . During the lives of the apostles the church remained comparatively pure. But “toward the latter end of the second century most of the churches assumed a new form; the first simplicity disappeared, and insensibly, as the old disciples retired to their graves, their children, along with new converts, ... came forward and new- modeled the cause.”—Robert Robinson, Ecclesiastical Researches, ch. 6, par. 17, p. 51. To secure converts, the exalted standard of the Christian faith was lowered, and as the result “a pagan flood, flowing into the church, carried with it its customs, practices, and idols.”—Gavazzi, Lectures, page 278. As the Christian religion secured the favor …
"For the mystery of iniquity doth already work: only he who now letteth will let, until he be taken out of the way."
Ellen White directly references 2 Thessalonians 2:7 in this passage.