The JW concept of the "Spirit-directed Organization" was one of the most troubling and perplexing problems which eventually led me to begin in-depth research. The organization is sold as an essential institution through which all people must gain salvation and even carry out their baptism. I simply saw no Scriptural foundation for this.
This concept tends to overwrite the New Testament's focus on the Holy Spirit. The Watchtower organization has appointed and sold itself as a form of indispensible "transmitter" through which the Holy Spirit is transmitted to Christians. No contact with the organization means no Holy Spirit. This concept is foreign to the Scriptures as it relates to Christians. The NT continually states that Christ is the one and only mediator. There is never any provision through which any earthly institution (organization) or group of people (144,000 / Governing Body) can share in that mediator role.
What also really troubled me was that the Watchtower requires baptismal candidates to verbally acknowledge being baptized into an organization before they can qualify for immersion. There is absolutely no Scriptural justification for this. First century Christians were never baptized "into" or as "members" of any particular congregation or the congregation doing the baptizing.
The other aspect that is so troubling about all of this is that the JW organization is proclaimed as the "ark of salvation" through which people must survive Armageddon. Nowhere in Scripture is there any indication that Jesus or the Apostles believed in this concept. The whole underpinning of one's salvation rested upon relationship with Christ. Nowhere was there any indication that one must be saved through a congregation or a collective group. Jesus' parable of the wheat intermixed with the weeds makes this clear. If Christ was talking about one true organization, he would have most likely used another parable or stated that there would only be one single stalk of wheat among the weeds.