I take exception to your assertion that "the researchers at our most prestigious universities" are for sale. I am not, nor have I ever been. I collaborate with geologists, biologists, and physical anthropologists, and none has ever been for sale - even those who've accepted private-sector funding (see below).
Your assertion that we were "a lot more independent back then" is not entirely accurate. I agree that industry-funded research should be viewed carefully, but (a) not all industry-funded research is, by definition, baloney and (b) not all research into transgenic crops is industry-funded.
Most of my research funds are federal (NSF), and none has come from a private company, but I've had friends and colleagues over the years who've gotten support from the private sector. In some cases, it was a disaster - they faced nondisclosure agreements and problems when their results didn't comport with the corporate message - but in most, it was actually very successful. And this was pure, inquiry-based research - not applied science.
And for what it's worth, my colleagues have reported similar problems working with NGOs and state-level agencies. Depending on the political winds, there may be pressure to support a particular party view. But if you've ever encountered a working scientist, you'd know that the vast majority are impossible to silence. We love what we do way too much for that. We may withhold some data if there's a publication embargo, and there are a few who've lost their ethical way (see, e.g., people with advanced degrees who continue to deny global warming; they're a tiny minority, but they exist), but the idea that large numbers of scientists can be made to toe a company line, for any reason, is laughable.
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