You are assuming that everybody in this system is honest: researchers, funders, and companies. None of these entities need to be honest to do research or to come up with topics. This is a big fallacy with academic research: nobody needs to be honest or truthful, and as much as you like to believe they are, they have no reason to be honest. I have experienced this first hand during my PhD life.
> Researchers are normally happy to do important things and they have good ideas.
That's not how research works, however---at least not what I experienced. Usually a goal is the prerequisite of the funding. If that goal doesn't align up with the interest of the company/or the funder, there won't be any funding to begin with. That's a lie that researchers tell themselves, that they have the freedom to work on w/e they find amusing.
> Academia being driven by money has less to do with academia and more with lack of money it needs to work on independent research.
Sure. If academia was a utopia that wasn't so dependent on money (and fame), science would take over. That utopia isn't anywhere in sight, however. Try going through academic job market: a popular question you get is how you are going to bring money into the university. If you don't have a good answer, you won't get a position. As a professor, you will be spending 80%+ of your time writing grants or, as you put it, begging different companies for money. The other 20% is spent on classes and bureaucratic headaches. A good professor that I knew had a long rant on how she never gets to do research anymore (from a very well known university).
People twist words and data to make their point, get a publication, make a name for themselves, get more money, and repeat the cycle, all in the name of research and science.
My point isn't that the academic people as a whole are bad, but many of them are trying to survive and are willing to do w/e it takes to bring in money. It is very easy to abuse the bunch when people are trying to survive.
All I am suggesting is that you need to be critical when reading academic papers. Regardless of the content, topic, etc. read and decide for yourself---if it is a field that you are proficient in---or read opinions on counter points.