Conflicts go well beyond just funding sources.
Here is where a collaborative effort comes in to monitor the responsible conduct of research by Institutional Review Boards and equivalents. Of course, these are mandated in publicly funded projects, and many institutions require independent review of other studies. It seems to me our best protections from these conflicts of interest lie in some oversight committee to whom these conflicts are disclosed and resolved, or at least actively managed. One need look no further than at the increasing number of retractions in the scientific journals in recent history to see the negative impact and relevancy of this issue. As a scientist who has worked for environmental organizations, I couldn't disagree more.