Can you go into further detail about this? I'd like to have more info about it in case it comes up in conversation, and I don't come off as someone who's pulling this out of his ass.
USAID was created by Kennedy in 1961 and was used to both give legitimate foreign aid to countries in need and also support his counterinsurgency/CIA operations against communists in the Cold War. Prior to that, the US had a bunch of assistance programs through the State Department and Department of Defense, but Congress got wise to this and cut funding because they did not want to spend the money. The CIA got hobbled as well by a number of Congressional acts and international conventions. So USAID became a way for the US federal government to filter money, technicians, and experts to specific countries in plain clothes. This was at a time when the USSR had a lot of money and doled it out to countries and insurgencies in hopes of winning diplomatic favor. Kennedy wanted to combat this.
Certain programs shifted in different ways. The anti-communist operations in Laos were originally State Department and DoD programs until Congress axed them; the CIA then took direct control of them. Vietnam programs were absorbed into USAID. After LBJ sent troops in 1964, the State Department and DoD operated openly, corrected a lot of the weird shit the CIA was doing, and improved on the shit that the CIA did right (e.g. Operation Phoenix).
I cannot speak to things that went on outside of Southeast Asia because I never read about or studied them, but most of what USAID/the CIA/DoD/etc did in SEA was on the nose even when it was under the radar. They weren't stealing shit, torturing innocent people for fun, or doing cowboy shit. The Pathet Lao and Viet Cong were terrorists killing innocent civilians in order to take over entire countries, they broke countless international conventions, and did all of this with assistance from the Chinese and the Russians. The prerogative of the Americans was to eliminate the communists more than anything else: the objectives and means to achieve them were pretty clear.
Most of the really awful human rights abuses that happened in Vietnam were committed by the South Vietnamese themselves - e.g. South Vietnamese police would take it upon themselves to torture Viet Cong.
When it came to USAID operations in Africa, specifically the Congo, they did everything by the book. Someone with more information about USAID operations in other countries can chime in.