This is a tough one because whenever you point to an individual (or group of individuals), the JW calls it an organization. Example, Noah. Noah should be a prime example of God working through an individual, not an "organization", yet the JW will tell you Noah and his family were an organization. In fact, they often use this as proof of God working through an organization.
Some points I've tried to make on this issue with dubs in the past:
Paul is explicit that he did not answer nor report to any so-called "first century governing body":
Gal 1:15-20
But when God, who set me apart from birth and called me by his grace, was pleased to reveal his Son in me so that I might preach him among the Gentiles, I did not consult any man, nor did I go up to Jerusalem to see those who were apostles before I was, but I went immediately into Arabia and later returned to Damascus. Then after three years, I went up to Jerusalem to get acquainted with Peter and stayed with him fifteen days. I saw none of the other apostles--only James, the Lord's brother. I assure you before God that what I am writing you is no lie.
Gal 2:1-6
Fourteen years later I went up again to Jerusalem, this time with Barnabas. I took Titus along also. I went in response to a revelation and set before them the gospel that I preach among the Gentiles. But I did this privately to those who seemed to be leaders, for fear that I was running or had run my race in vain. Yet not even Titus, who was with me, was compelled to be circumcised, even though he was a Greek. [This matter arose] because some false brothers had infiltrated our ranks to spy on the freedom we have in Christ Jesus and to make us slaves. We did not give in to them for a moment, so that the truth of the gospel might remain with you. As for those who seemed to be important--whatever they were makes no difference to me; God does not judge by external appearance--those men added nothing to my message.
Also, ask the jw which organization God was working through when David left the nation of Israel to live in an enemy nation. Or when Joseph was in Egypt.
Here's a link to a great article by Tom Cabeen, titled 'Does God Work Through an Organization': http://www.caic.org.au/jws/organization/godorg1.htm
TS,