Nope, religion still exists in the future. It's not going anyway until we rewire our neural pathways to stop giving people feelings of religiosity. For now I'm going to start with the one I have the most familiarity with. Maybe someone with more exposure to others could pitch in? You know, if this forum isn't dead. :P
Neo-Christianity has its roots in Christian reform movements in the Association of Stored Humans, the Nanori, and the League of Independent Worlds. These movements sought to reinterpret the doctrines of the Churches in Exile to accommodate the existence of digital intelligence. A great deal of this debate was rooted in the question of the soul, and whether or not digital intelligences possessed one. This question was of particular importance among Stored Christians whose culture emphasized what they spoke of as the "inherently suicidal nature of brain uploading."
Interpetations still vary, and fundamentalist strains of Christian thinking persist in habitats among the Independents and in the United Planets of Mechanica. However, reformists have managed to put together a set of generally agreed upon interpretations that they feel provide spiritually genuine accomodations for digital intelligence. According to Neo-Christian thinking a DI created by mankind begins without a soul. However, a DI may acquire a soul at the behest of God by undergoing baptism and taking on a designation which ties them to Christian life and culture. In the event of the total destruction of the DI's code due to hardware failure or erasure the baptized DI will go on to judgement as any other Christian would.
However, actively seeking to become a digital intelligence is generally considered to be a form of suicide except among the most liberal interpretations of Neo-Christian doctrine. The soul of the uploaded human goes on to judgment, and the DI created in their image by the process is considered a spiritual blank slate. It is without sin, but lacks a soul until baptism.
Christians from the Association of Eternal Life experienced further upheaval compared to others due to the metaphysical dilemma created by existing as many selves at once. This has resulted in the founding of the Church of the Manifold Spirit, who hold that the soul is a numinous thing unbound by flesh which extends itself into any and all instances of a person present in God's creation. It is only when no version of the self exists in the universe that the soul is subjected to judgement.
Neo-Christianity still struggles to accomodate group mind configurations into its doctrines, and psychohistorians are predicting a crisis point for the religion coming from this issue in the near future.