It seems to me that the problem here is that our industry, built around throwing expensive drugs at problems, paying for results and lobbying governments and insurance companies is ripe for abuse of "science".
That said, "pure" science is about more than published papers: it's about taking the data and observations you have and constructing the most likely theories and explanations around the observed evidence. If we had a capability to separate funding (and emotions) from research we might be able to produce good results given enough open data (which is itself a challenge).
As an uninformed software developer, I think medicine is a field where machine learning based tools will shine: ethical ("hippa") issues aside, we eventually might be able to feed all observed data, from diagnosis to results years after treatment into computer systems which might be able to make sense of the data and allow us to construct conclusions of the data unbiased by personal and business incentives.
Obviously our current eco-policital climate is strewn with roadblocks, but just wanted to put it out there that science doesn't have to lead us down this path if done right.