The MSF [link|http://www.doctorswithoutborders.org/pr/2004/07-28-2004.shtml|press release] explainins their reason for leaving.
A key point of it being
...on May 12, 2004, MSF publicly condemned the distribution of leaflets by the coalition forces in southern Afghanistan in which the population was informed that providing information about the Taliban and al Qaeda was necessary if they wanted the delivery of aid to continue.