Just World Theory stands in contrast to sound doctrine, but could be deceptively similar to the undiscerning. This is because the Bible depicts a just and righteous God who executes judgments for sin and evil. The missing piece in comparison would be the doctrine of God's longsuffering nature. The Scriptures indicate that God is slow to wrath or anger. 2 Peter 3:9 says, "The Lord is not slow about His promise, as some count slowness, but is patient toward you, not willing for any to perish, but for all to come to repentance." Another great biblical example is the Genesis 15:16 implication from the "sin of the Amorites" not reaching its full measure, that God tolerated the sin of the Amorites for 400 years before bringing judgment (the full measure attained).
We also know from study of the Bible that God brings trials and testing even on true believers. The whole book of Job tells the story of how God allowed the testing of Job's faith by Satan. The many losses that Job endured were caused not by the sin or lack of faith of Job. Trials by fire are understood biblically as refining us like as done to silver or gold. The replies of Job's friends, such as Eliphaz (Chapter 4- "the innocent do not suffer") and Bildad (Chapter 8- "God rewards the good") are in favor of more of a Just World Theory. However, by the end of the book, God explains that He is displeased with Job's friends for what they said, and that they have to present sacrifices to atone (Job 42:7-8).
All of this being said, Just World Theory itself has internal logical problems, where if one follows through with logical consistency, it produces conclusions that are inherently bigoted or absurd. For example, in Just World Theory the African slaves themselves are to blame for the early American slave trade- either collectively, or by each individual, they must be or have done something wrong. This bigoted conclusion could further lead to the scapegoating of an entire race for their plight- blaming their own evil (specific to them only) for the evil they are going through. We know this is not true. All men are born equally with original sin. As Christ said in Matthew 5:45-46, "for He causes His sun to rise on the evil and the good, and sends rain on the righteous and the unrighteous. For if you love those who love you, what reward do you have?"
Taking, for example, the oppression of the Israelites as slaves in Egypt, if there was even a moment that God was not pleased that they remained in slavery, yet they still remained in slavery, then wrongful oppression is possible on earth. Exodus chapters 3-14 reflect that very situation, ending in judgments against the Egyptians to free Israel. For that period of time the Hebrews remained in slavery with the Egyptians while God did not approve of it. The Bible reflects a view where oppression is not to be taken lightly, but examined and called into question, if not even fully interfered with and ended.
Another obvious internal problem with Just World Theory is that it justifies lone acts of violence. This would be true, since anything that happens to a person is supposed to be just from a higher level of strata. Therefore a person victimized by an act of violence is blamed in Just World Theory either for their own evil, negligence, or lack of preparation. This further results in absurd conclusions, such as that school shooters are ethically justified. In the era of guns and other technology, the madness and rage of just one individual can unleash harm on a whole crowd of others. Too bad for these Just World adherents that "might makes right" is a logical fallacy. Adherents of the Just World Theory are themselves responsible for answering as to why they are holding to an ethically degrading view, such that results in bigoted conclusions, and justifies oppression and lone acts of violence such as school shootings.
Since Just World Theory is not a view really taught in churches per se, and is more properly understood as being from Eastern religions, it has become fodder for studies in Sociology and Social Science as to who adheres to these biases demographically. (I mean, let's be fair...how did that view ever spread in the U.S. and to who?) I see it as a country bumpkin theology to which Protestants are susceptible, but to which we're not supposed to be. It's a way of explaining away life in very easy, neat, and tidy terms justifying not only one's own position in life ("I got there by my own striving and hard work"), but explaining away the plight of others as something not to worry about so much, since they could be to blame in Just World terms. While this would seem to be a neat shortcut to avoiding personal guilt in one's outlook, it is not respected as properly correct in biblical terms. Just because there is a God who is just, righteous, and true, it does not follow that we live in a perfectly just world as described by Just World Theory.