Everyone keeps saying that they violated the terms of the agreement, but from TFA, I'm not so sure that's the case. The agreement said that the blood would be used to “study the causes of behavioral/medical disorders”. Most of the research described seems to fall under that category. It was originally presented as work to help understand the high diabetes incidence in the tribe, because that was why the blood was collected in the first place, but when that work was done, they still had the DNA. Why not do research to the full extent covered under the agreement? It would have been more polite, perhaps, to for the various researchers working with the samples to keep the tribe updated on their work and findings, but nothing in the agreement required that.
Regarding your insistence that this was a violation of "do no harm" - I'm not buying it. I understand it's place in medical lore, but if you think it's really a useful guide, you're wrong. If "do no harm" was truly a useful rule for guiding doctors' actions, then they could never perform surgery, they could never prescribe drugs with harmful side effects, and the entire structure of medicine as we know it would cease to exist. They have to do some harm; the question is whether the harm is outweighed by the benefits. "Do no harm" sounds nice, and as a sort of generalized medical philosophy it's salutary, but it's so vague as to be useless for actually making decisions. That why, when doctors are actually looking at the ethics of their decisions, they don't ask "Did I do harm?". They look to the rules of medical ethics which have been developed through a lot of hard work by people actually dealing with real-world problems. Much as with science generally, relying on the writings of people who have been dead for thousands of years rather than your own judgement and the evidence is a terrible idea.