The article on this actually somewhat distorts Kerry's comments. First, it is very clear that he is concerned about the "good governance". So, the idea that he is convinced that Karzai is going to move from corruption is a complete overstatement. It is more that JK says Karzai knows that the US is demanding that.
On the CIA connection, Kerry did speak of the meeting with Panetta, and pushed back on Karzai having a "direct relationship", but his point was that Congress needed to know. (He did say that there were times the public should not know - they have to be secret.) Kerry does think that him working for the CIA is a problem.
On Clinton, his answer was much further, pulling the answer away from Clinton to what we are trying to do. As in the article, he completely avoids the chance to say anything negative.
This is a good, very thoughtful, serious interview. In fairness to the article, I can see why it was written as it was - those were the two points that were most noteworthy. I think they should have qualified Kerry's confidence in Karzai to indicate that Kerry was clear there was a lot of change needed. (even confidence is overstated as it certainly would not build trust if Kerry returned to the US and spoke of doubts about him changing. From his words, phrasing and demeanor, it is clear that he is aware of the problems.
Anyway -
http://www.bloomberg.com/apps/news?pid=20602085&sid=aQX6DUsOKIeI(click on the link under Kerry's photo)