Only those elements of the national police that the chief of the national police does not oversee? That's not very comforting. Given the evidence available, Tigre looks like it might be the unit cut from US assistance.
Greg Weeks at Two Weeks Notice has more on the role of a human rights agenda in US foreign policy. Given what the US cares about in Honduras, concerns about drug trafficking should trump human rights concerns. However, in this case, aid is being suspended because the chief of police might have been involved in extrajudicial killings years ago. Aid is not being suspended because Bonilla was involved in drug trafficking, was corrupt, or incompetent in carrying out his duties. Those might all be there case, but for now, they are not.
A few more things about the story. I don't think that the letter from US and Honduran academics and members of the US Congress caused the State Department to do something that it didn't want to do. I wouldn't go so far as to say that it's just a coincidence, but there's got to be more to the story, obviously, than what we already know. For example, what the State Department did isn't exactly what the letter writers asked them to do. (Here's the letter.)