Are PRTs a threat to the legitimacy of Afghan government?

The Afghan president, Hamid Karzai, has recently been talking about getting rid of PRTs (Provincial Reconstruction Teams), which were originally operated by the US military forces partly to win hearts and minds, arguing that they undermine the role and legitimacy of the Afghan government in the eyes of the Afghans. Here is some background. While I couldn't agree more with his position, I can't help but wonder if this is truly the most important factor that undermines his government legitimacy. The Afghan government has bigger threats to its legitimacy, including but not limited to Hamid Karzai being literally "chosen" by the United States after the overthrow of the Taliban, extreme aid dependency (in 2007, about 90% of Afghan government budget came from foreign aid...with little signs of improvement even now), controversial elections, Afghan military control certainly not extending beyond Kabul and even in the capital highly dependent on ISAF, and the like.

So are PRTs a threat to the legitimacy of Afghan government? Yes, but it's a small drop in a bucket.