"If a brother is starting to look at material on the internet and starts to have serious doubts about the JW organisation and questions the integrity of the governing body. What steps would be taken to by the congregation to readjust his thinking."
The congregation in the Jehovah's Witnesses has no power; it is the elders that deal with such matters. They are likely to simply form a judicial committee and interrogate the person as to whether he still believes that the "Faithful and Discreet Slave" is Jehovah's organization.
"And also if the congregation is not aware of this but he has confided in an individual how would that individual try to help such a brother?"
That individual will snitch on him to the elders. Just confiding anything to an individual will be considered causing "divisions" as the apostle Paul mentioned in Romans 16:17. That could easily be a disfelowshipping issue.