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.
Yes, MSF did state what you excerpted, and no doubt those statements by the US made their task more difficult. But the final paragraph of the press release seems to list their main reasons for leaving:
Humanitarian assistance is only possible when armed actors respect the safety of humanitarian workers, more than 30 of whom have been killed in Afghanistan since the beginning of 2003. The killing of our colleagues, the government\ufffds failure to arrest the culprits, and the false allegations by the Taliban have regrettably made it impossible for MSF to continue providing assistance to the Afghan people.
Re: The last paragraph might be a better summation.
Was just trying to keep it brief and leave it for the reader to evaluate the whole statement. However, it cannot be ignored that the Taliban's allegations against MSF don't occur in a vaccum and are reinforced by the US tying aid with the 'winning of hearts and minds' and capture of the Taliban.