Quite a few people left with HRC because they were Clinton's people, who were more interested by being seen with her than with foreign policy. Others left for better opportunities after 4 years.
I understand why some people would want all these positions manned quickly, but the truth is that you do not find that many competent people (particularly if not being connected to the WH and the Clintons is a worry for Kerry) that quickly. (and do not discount that some friends of Ms Rice may be doing some sabotage as well at the WH level.).
I would not worry about the article, which is more a warning call than anything else, and hopefully, will catch the eye of the White House and make them move.
Two points I find more problematic in this report than the latitude Kerry has to name his people (this is more of the same "he is not Clinton" crap).
a/ I am not familiar with Chris Nelson, who seems to be largely the basis for this report. He is well known in Asian policy circles, but it is hard to know what his motives are. (which does not mean that there are not too many seats empty at the State Department. I was surprised that the nominations did not go any faster, even if Kerry has been largely absent throughout March).
b/ I really dislike the notion that Ms Nuland is gaining influence. Hell, she was one of Cheney foreign policy advisers. Her BIL is one of the architects of the Iraq War. Her husband is a neo-con. It is Clinton who named her where she is. If anything, I took the notion that she was replaced by Psaki as positive. I certainly do not like the idea that Nuland and people like her may gain power, in particular in these dangerous times.