The only effective solution I see is making fraud harder to hide. (There’s also making the penalty for fraud higher and trying to instill integrity, but the problem is some people will still take the risk.)
The reality is these negative results are just as useful and can either help other researchers avoid dead ends or they might have a not great result but with some refinement to methodology might be worthwhile for further study.
Researchers should be judged on the quality of the research they perform, not their outcomes. A well crafted study that shows that further research shouldn't be done should be just a well received as a well crafted study showing more research should be done. The focus should be on the design of the study first, since no matter what the results it adds to the corpus of knowledge in a meaningful way
Only in academia is fraud treated as a faux-pas rather than a crime. We have accepted a status quo in which academics and academic institutions play by a different set of rules to the rest of society. As a result, hundreds of millions of dollars are being wasted and patients are suffering real harm. Academic independence is valuable and should be protected, but independence does not mean impunity.
2. Letter-writers have no control over the work of the person they recommend. They cannot prevent the submission of a manuscript or a grant. They would be taking a lot of risk for no gain.
3. Letters of recommendation are a form of corruption and nepotism. If you would have a conflict of interest for reviewing a manuscript or a grant, you should not be allowed to write a letter of recommendation either.
This is absolutely false in real science and that you say it seriously is proof of just how far gone the academy is. Needless to say no matter how much you fake your data or results, nature is not so easily fooled.