Why do Christians still struggle with sin? Why does God allow it to remain and not kill it immediately like he will do when we see him face to face and reach our glorified state? Every believer has asked these questions when the war against flesh and Spirit becomes tiring, but they are not without answers. Below, Thomas Boston gives seven reasons sin is not immediately eliminated from the believer’s life.
1. God has ordered the matter of the believer’s sanctification that sin is left to be active in their souls while here on earth, for their further humiliation. For example, God gave Paul a thorn in the flesh to keep him humble. And so we find David, after his grievous fall, grows in the grace of humility.
2. The Lord allows sin to remain in His people so they are stirred to the frequent exercise of prayer. The soul feels the continual need of pardon, and therefore must be much lying at God’s footstool. When His children grow remiss in their duty, the Lord sometimes allows them to fall into some grievous sin to awaken them and wound their conscience, so that they cry to Him like a child who falls into a fire.
3. The sin left in us makes us more watchful of our hearts which still are prone to wander. When a prisoner escapes, and they catch him, they will put him into more close custody than before. We walk through a world filled with many snares; if we were not watchful, we would be caught in them!
4. Just like God allowed some Canaanites to remain in the land to try His people, so He has left remains of natural corruption in them for their exercise and trial. Indwelling sin makes us lean on Christ’s strength and use God’s armor in the battle.
5. Through sin is left in us, we are made more and more to feel our need for Christ and His precious blood for the removal of our guilt daily contracted anew, and for the strengthening of our souls in our Christian course so that we come out of the wilderness resting upon our Beloved.
6. Through the indwelling sin that remains, Christ is glorified. While the enemy, sin, dwells in us, Christ’s grace and Holy Spirit are at work in us so that the enemy cannot overcome, domineer, or destroy us. Because of indwelling sin, we know that we cannot justify ourselves, but can only be justified by the perfect obedience of Christ, which we lay hold of by faith. In this, Christ is glorified.
7. To see how God makes such an excellent medicine from such poisonous ingredients, cannot be but very delightful! Romans 8:28
-Thomas Boston
The Fight of Faith 
Far be it from me to challenge a theologian like Tomas Boston but I humbling disagree with the main premise here.
Paul’s “thorn in the flesh”, “a messenger from Satan” was not sin, but a tribulation, a devilish harassment certainly not of his choice.
God allows tribulation, illness, oppression and suffering as painful refiners of our faith.
But sin is upon us to repent, to turn away from, even to expel from among us.
I can hardly believe that God “allows sin”, as though permitting it. As soon as I’m drawn to sin, the Holy Spirit, in love, will warn me. He’ll warn me again. If I refuse God’s call, He will stop warning, my heart will turn away and believe me – I will reap what I sow.
God didn’t sit back and, for example, allow my husband to commit adultery. He warned him, pressed heavy upon him, then finally abandoned him to his sin until his life was crushed.
From my scriptural study and experience, it is not God’s will that sin remain in us. He actively warns, purges, and prunes us because He loves us.
Of course we will never be perfect, but its a road toward holiness. In this He allows us to struggle and wrestle but I can’t see that He wills sin to remain.
LikeLiked by 1 person
I agree with your points, especially your point about the “thorn in the flesh,” I thought that was a bit odd. I also agree with everything else you said. We are called to fight sin and the Spirit works to warn and guide us when it is active. However, the reality still exists that indwelling sin is part of our existence in this life even as believers, and one day God will bring it to an end, but that time is not now. In his wisdom, we can be sure that he has good reasons for not eliminating it now.
Thanks for stopping by,
LikeLike