There's a very interesting story on the NY Times about Harvard medical school and ethics as it relates to relationships with industry. We're primarily talking about the pharmaceutical and biotechnology industries, but we must also remember medical device and diagnostic equipment companies. In any case, Harvard professors are deeply involved in industry-funded research and many of them are also paid speakers and consultants for several of these companies. Conflict of interest is the key buzzword (or in this case, buzzphrase). How do you resolve any potential conflicts of interest in such situations? It can get quite complicated, especially if you have significant ties to industry. However, I believe that it can be done, but that's not to say that everyone out there is doing it correctly.
There have been many stories of highly-ranked academic professors quitting their academic careers to work for industry. I think people need to find what's right for them, and for some, a career in non-clinical medicine is the right fit. I personally know several people who have transitioned from academia to pharma and most of them seem to enjoy the different challenges and rewards faced in a corporate environment. Of course, there are pros and cons to every decision, including the decision about leaving academia. The bottom line is that it's a very personal decision.