The scientific method and scientific endeavour in general is not the same as the conduct of individual scientists. I read a great article today talking about that point, and I think it is worthwhile reading for anyone who wants to learn about the way the science community deals with fraud, shoddy work, and wishful thinking.
Primarily we need to separate the basic concept of investigating ideas thoroughly and rigorously by trying to falsify them from the actual practice of real people in messy situations.
We want to look at our ideas and hypotheses critically. We should do our best to try to prove them false and only declare them true when all attempts to show them false have failed. Working hard to test our beliefs and building a model to understand the universe around us based on these principles is science at its core.
There will be scientists who get things wrong. There will definitely be reporting of science that is grossly mistaken. Just because those things exist doesn't mean the whole endeavour itself is somehow pointless, dirty, or mistaken. It just means we have to be careful whenever we have human beings interacting with a system that we know works.
The scientific system of inquiry doesn't care about grant dollars, or egos, or employment. People do, so let's keep that in mind.
Also seriously, can we get away from p=.05 as a standard? Artificially squeezing results in to fit that standard of proof is such a mess. I don't claim to know what standard should replace it, but surely we can find something better.