Here's the problem...

When you don't actually discuss things beforehand you wind up just giving into the most aggressive group. Nine times out of ten, that aggressive group is filled with idiots and nut cases who want to ignore everything that does not support their argument and so you get crap science that mostly contradicts itself and in the end is useless for anything but garnering more funding.

Because the people who insisted on the funding in the first place are basing their careers and reputations on finding the exact outcome they claimed they would get, they have to throw scientific method out the window and don't ever dare admit they were wrong and have no choice but to attack anyone who questions their methods or results.

So you get nut cases trying to deoxygenate the ocean in an attempt to lower CO2 levels. a brief discussion would have pointed out just how insane the attempt was, but the scientist in question received funding just by asking around. THe only reason we're not in a soylent green scenario now is the ocean is a very big place.

To your implication, I do not think it is possible.  Assessing data and isolating pertinent facts is a learned skill.  Most engineering and scientific degree programs spend a lot time simply teaching students how to solve problems through rigorous methods.  The average person does not have this training.  Expecting the average person to identify, isolate and remove their emotional and confirmation bias before approaching a problem would be like expecting the average engineering student to be good at arc welding.  If a person has not been trained in a skill and/or has not practiced it, we cannot reasonable expect them to be good at it, regardless of the person or skill in question.

I believe (though probably cannot easily substantiate) that the issue only gets worse due to our own opinion of our opinions.  I feel people view their opinions as an extension of themselves; attempting to show that an opinion is unsupported by fact becomes equivalent to attack the holder of the opinion.  This is in contrast to my arc welding example above.  A college student may not like being told that their arc weld is poor, but I believe most would realize that in describing the weld as poor we are not personal attacking them.  As the opinion holder comes to feel that they are being attacked, they will defend themselves and become futher entrenched in their opinion.

While training everyone in standard problem solving techniques might solve the problem, this is no more likely than teaching everyone to arc weld.

I am an engineering professional who has worked in manufacturing environments for over 25 years.  I have been involved in numerous efforts to engage manufacturing line workers in problem identification and resolution efforts.  It is often extremely difficult for them.  They are not 'dumb' people, many are quite bright.  But while we, as scientists and engineers, have been practicing solving problems for years - they have been practicing various manufacturing skills for years.  We can no more impart our problem solving experience to them in a week than they can impart their manufacturing skills to us in a week.

My opinion again, likely both poor communication and lack of foundational knowledge play into it.  But I strongly suspect it is a thrid thing.  I am trying to recall the reference and it escapes me, but the phrase is, "Each of us speaks from his own pain."  When I hear most people argue an opinion, they are not arguing on fact, but arguing on how they wish things were.  It's an easy trap.  Part of the training that engineers and scientists go through addresses that our wants, hopes and dreams do not trump fact.  I must acknowledge that as pragmatic as I am, I catch myself drifting into that territory from time to time.  This is especially true if the argument concerns something that affects me or those close to me.

Using the article's example of the National Bio- and Agro- Defense Facility - it is easier to analytically weigh the pros and cons of a particular build site for such a project when the proposed build site is not across the street from my home.  As long as it is in someone else's backyard it's just a numerical risk assessment vs. gain assessment.

In turn, I doubt the federal government is holding nationwide discussion on the NBADF; I am betting that the community discussions are being held in the six target locations.  The people that come to those meetings have more of a personal stake than the rest of us.  Their personal stake does not change the facts.  But it likely makes it more difficult for the local population to focus on those facts.

One way to maybe break through this is to force each group to defend first their side of the argument, then the other.  We had to do this back in middle school for some class, and if you take it seriously enough, you start to see the merits of the other argument.

Also, as a Wolfpack graduate, I'm proud to see an article from NC State on here