This isn't OT at all since most HN readers won't be CEOs of publicly traded companies. Your situation is far more common.
A good guide for this is how the FDA manages Good Manufacturing Practice (similar to ISO 9000 except focused on, you know getting shit done instead of getting hung up on the process). One important part is the distribution of responsibility. They get extremely upset by situations like the one you describe specifically because of the possibility of undue influence on the results. Manufacturing, R&D, QA and QC have to be organized to ensure proper independence.
(Which also means if you hear about scummy behaviour from a drug company: that flows from the top).
-d
PS: little known fact: the FDA has armed enforcement personnel who WILL storm through the door in some cases where they believe fraud could be involved in endangering people. I know of cases of this on the pharma side at least -- the food side may be more lax.