As someone in science, I can safely say, the scientific method has not changed. And that is definitely not how it works.
The biggest issue here is the media plays into single-study syndrome. New information must be taken in context with what is already known and conclusions shouldn't be stretched beyond what the data supports (as they often are in click bait headlines). But based on your assertions, the most science you seem to see is directly out of the Today show. Try reading the original works sometime - they don't stretch conclusions beyond what the data supports - it's University PR and the media in general who do that. And it's the public who have been led to believe that science advances in leaps and bounds, when in reality (for the most part), it advances slowly and piecemeal.
As for your conflict of interest mumbo-jumbo - just because someone has a stated conflict of interest doesn't mean the data is automatically bad. There are a lot of great scientists who work in industry and it annoys me, as an academic, to see people besmirched just because they happen to want to also make a paycheck while doing what they love (I don't know if you've looked, but tenure-tracked academic positions are few and far between, and pre-professor salaries are abysmal compared to the private sector). There are companies and individuals guilty of doing bad things, but if anything, most companies want their products to be scientifically valid - they have a vested interest in making sure it really works and not just faking it.