If God Is Sovereign, and God Hates Sin, Why Does He Permit Sin?

In 1766 John Newton wrote a letter to his correspondent in which he honestly observed "the remarkable and humbling differences" between Christians' "acquired [knowledge] and their experimental knowledge, or, in other words, between their judgment and their practice." (You can read most of the letter here.)

A Christian knows that communion with God in prayer, faith, and the Word should be our sweetest delight, our exceeding desire. But in reality, these are often difficult for us. Newton writes:

Though he knows that communion with God is his highest privilege, he too seldom finds it so; on the contrary, if duty, conscience, and necessity did not compel, he would leave the throne of grace unvisited from day to day. He takes up the Bible, conscious that it is the fountain of life and true comfort; yet perhaps, while he is making the reflection, he feels a secret distaste, which prompts him to lay it down, and give him preference to a newspaper." [You could substitute the word "website"!]

But then Newton turns to a perplexing question indeed:

How can these things be, or why are they permitted? Since the Lord hates sin, teaches his people to hate it and cry against it, and has promised to hear their prayers, how is it that they go thus burdened? Surely, if he could not, or would not, over-rule evil for good, he would permit it to continue.

Here is how he answers:

By these exercises he teaches us more truly to know and feel the utter depravity and corruption of our whole nature, that we are indeed defiled in every part.

His method of salvation is likewise hereby exceedingly endeared to us: we see that it is and must be of grace, wholly of grace; and that the Lord Jesus Christ, and his perfect righteousness, is and must be our all in all.

His power likewise, in maintaining his own work notwithstanding our infirmities, temptations, and enemies, is hereby displayed in the clearest light; his strength is manifested in our weakness.

Satan likewise is more remarkably disappointed and put to shame, when he finds bounds set to his rage and policy, beyond which he cannot pass; and that those in whom he finds so much to work upon, and over whom he so often prevails for a season, escape at last out of his hands. He casts them down, but they are raised again; he wounds them, but they are healed; he obtains his desire to sift them as wheat, but the prayer of their great Advocate prevails for the maintenance of their faith.

Farther, by what believers feel in themselves they learn by degrees how to warn, pity, and bear with others. A soft, patient, and compassionate spirit, and a readiness and skill in comforting those who are cast down, is not perhaps attainable in any other way.

And, lastly, I believe nothing more habitually reconciles a child of God to the thought of death, than the wearisomeness of this warfare. Death is unwelcome to nature;--but then, and not till then, the conflict will cease. Then we shall sin no more. The flesh, with all its attendant evils, will be laid in the grave. Then the soul, which has been partaker of a new and heavenly birth, shall be freed from every incumbrance, and stand perfect perfect in the Redeemer's righteousness before God in glory.

Newton goes on to answer the question of how such sin can be mitigated or overcome. I won't quote the rest of the letter, but simply this line which sums up his positive counsel: "Faithfulness to light received, and a sincere endeavor to conform to the means prescribed in the word of God, with an humble application to the Blood of sprinkling and the promised Spirit, will undoubtedly be answered by increasing measures of light, faith, strength, and comfort; and we shall know, if we follow on to know the Lord."