I think there's a subtlety which isn't implicit in what you say. There is the ideal of science - which I think there's a case to be made that it's not something that can be fixed, but constantly evolves - and the practice.

But I think there's also a separate distinction between good faith and successful enough attempts to do science, and people just gaming the system. The fact that there's plenty of the latter must be acknowledged (in fact, I think the people who discovered this current set of issues and made a big deal of it are from the same group of academics as the ones abusing this loophole, and also, it's likely to be a perennial problem), but the former also exists and is not the same as the abstract ideal you bring up.

I'm not sure I would characterize Sagan's system here as specifically best expressing the scientific ideal. I think it's a great list to think carefully about to help with clear thinking, but I'm not sure applying the label of 'science' to all these points is the right way to think about them, although I'm not sure it isn't either.