Forgive the length of this post, but your post struck a cord with me. (TL;DR: Father was a convict, saved, well-read in theology and the word -- rejected many times by the church. I believe we are called to embrace these men and women)
My father was an ex-convict. As a child, I did not really understand the social implications of his previous life. However, as I grew up, I started to see the reason why certain parents of my Sunday school friends would not let their children play with me or my siblings. I came to understand why there were elements of many churches my father was considered an "exile".
My father admitted that prison was the best thing that ever happened to him -- he said without it, he would most likely be dead. This held a dual meaning. He meant that literally, had he continued his lifestyle, he would have died. He also meant that in prison, he found Christ -- his rock, his anchor, and his redemption.
My father began his journey of sanctification and justification in maximum-security prison, surrounded by drugs, by violence, muddled in the brutal reality of humanity without the hope of salvation. As much as the stories of his time in prison depressed me, I was broken-hearted to hear how the church had treated him. Before he passed away, I witnessed how hurt he had been by the church. I saw what the people he had trusted and respected had done to him. The church, above all men, had proven to him that people are flawed and in need of salvation.
He was a man versed in theology. Among his favorite authors were Sproul, Lewis and Tozer. He had a voracious appetite to serve God, and he strove to do that. He was well-read beyond many of his peers in the church. He experienced a depth and dependency on Christ that so few can comprehend. He defied convention, but he was still rejected by the church many times over. He had his flaws, certainly, but he had shunned his former life, embraced the pursuit of Christ, and committed his life to serving the Father.
In the end, your story about this man is compelling. Please, for the sake of this man and men on the same path like my father, continue to love him well. Understand that through prison, there are deep wounds and a permeating darkness that only the Lord can truly heal. However, that does not negate the value of Christian counseling, of Christian friendship, and of intentional Christian community.
I have been so frustrated by stories like this and that of my father. We are the BODY of Christ, we are the disciples of the Creator, we are the PRIESTHOOD... are we not called to welcome these prodigal sons back into the body with open arms?
I will pray for your relationship with this man, for his continued growth towards Christ. That he can one day find a church that will embrace him -- knowing his sin, and show the true mercy and compassion of the Creator. In the meantime, may he ever walk towards his loving Father.