" In the Tuskegee case, it started in 1932 and only ended 40 years later in 1972. They managed to keep that one secret for a long time."
Aside from publishing research papers in journals, of course. It was that secret. What would the point have been had they not published?
Yes, it's an appalling story, but I'm still not quite clear what point you're making. At the outset it was not ethically dubious. Although the way they secured consent for spinal taps was bad, it was no worse than the way Andrew Wakefield did it seventy years later. Fifteen years after the programme started, the ethical situation changes because although at the outset there had been no treatments better than those on offer, now there were. That was the ethical failing: the first fifteen years were either fine ethically, or at worst marginal (the agreement to withhold additional treatment from conscripted men is arguable, given the treatment that would have been given was no better than placebo).
It goes horribly, savagely wrong in 1948, when penicillin is available (although it's worth noting in passing that given the US's lack of healthcare, it's not at all obvious that black men in the deep south who weren't enrolled on the study would have done any better) and it should have been stopped. But by then it's a run-on research project, started many years early, operating on a care and maintenance basis, with an assumption that if it was OK last year, it'll be OK next year? It should have been stopped in, at the latest, 1966 when the CDC became aware of it, and that was a failing by a government body that was, rightly, excoriated when it all became public. But there are other trials which, when started, were ethically OK, but drifted into badness later (the radioactive chapati flour scandal in Coventry in the 1950s, for example: it's a lot more complex than it looks at first glance).
No one would argue, I hope, that governments don't sometimes do wrong. But I don't believe that's a result of "government" being indifferent; it's usually the result of people with a focus on one topic not seeing the whole picture.