Because this is still such a fundamental for Bride candidates, here's a brief on the sector of Mystery Babylon that is the Christian Church. This Babylon is a mixture of the holy and the profane. In the process of separating out the holy, the Lord takes us out of Babylon and then He takes Babylon out of us. At some point, when there is enough distance, we get a startling revelation about its character. The carnal mind can't grasp the self-contradictory reality. We can only accept it as the Lord reveals it. The lies of the profane imprint over the truth, being conveyed along on the truth like a wrapped package, like a glove on a hand.
If you still can't accept what I've been describing, you have not yet received the insight which only comes by revelation. Seek the Lord about drawing you near to Him, in holiness.
The church authorities have been been appointed and established by the authority of the sovereign God, like the governmental authorities. The Lord knows the extent of the corruption - He ordained that it should be so.
Another simile spake he to them: `The reign of the heavens is like to leaven, which a woman having taken, hid in three measures of meal, till the whole was leavened.' ~ Matthew 13:33 (YLT)
The Lord has a plan for Mystery Babylon. Its end will come in due time, and justice will be served; but that time is not yet because the necessary work is not complete. This is a sifting, testing, a purification work - and the Lord is getting what He desires, what is pleasing to Him. The Lord is preparing a sacrifice, a people who are worthy. His character as Love will manifest. He is righteous and good and just, and sovereign. Do you trust Him? Can He trust you?