I found an interesting article written by Hugo Slim about the implications of aid agencies that work in areas with poor government structures. The author states that: "providing or enabling social and economic development is obviously a public good but, simultaneously, it can bring about political harm."
I agree with the author in that communities can become dependent on aid agencies and miss opportunities for self growth, and where if possible aid agencies should try to work with governments and deliver support through them when possible.
You can find the article at:
http://www.globalpolicy.org/ngos/state/2007/0412hugoslim.htm