I do agree with you that the situation is not ideal in any way and I would prefer it if science could rely wholly on government funding without the necessity of justifying its productivity. Whilst I have much less experience than you, I did work with a scientist during my gap year and he made a point of discussing these kinds of things with me. He had experience both in postdoctoral research in an academic and commercial enviornment, finding that neither was truly ideal and that wherever one went there was fierce competition for limited funding opportunities.
The general public is becoming more aware of science and, as a result, science now has to contend with being able to justify itself to the media and to accountants, whether they work for private companies or the civil service. As ever money has dragged us kicking and screaming away from the ideal situation to somewhere where pragmatism reigns and the people running research departments tend not to be the best scientists but the most determined and savvy individuals who are capable of acquiring funding.
I do think that the patent system has something to offer in terms of incentives for entrepreneurial inventors most especially, as well as driving corporate R&D, though its rather stringent pre-filing secrecy requirements seem a little excessive.
It does seem that scientists now have a lot more to deal with and it is with some trepidation that I look forward to a career in science, but at the same time I think it is good to force scientists to look in a more critical fashion at their research so that we can tackle wider problems and provide a valuable service.