"I don't think scientist are so much hurt as lost: when you have years of evidence pointing in one direction, and someone replies with a completely unscientific argument (take a lot of pseudo-science for example) what is he supposed to do?"

My suggestion as to what the scientist is supposed to do when encountering a completely unscientific argument is below. Please note, I am not trying to respond to any of the other aspects or questions you asked -- this "simple" response became way too long as it is :-)

PREPARE AHEAD OF TIME:
A. Learn to communicate. A lot of life is dealing with miscommunication. It seems scientists as a group have the same issue with miscommunication that software developers generally have. This is very important where the science is critical for impacting public policy decisions. Especially, learn to listen, so that the metaphors and analogies that are guiding the incorrect thinking can be ascertained.

B. Expect that as soon as you are using science to advocate for public policy changes scientists will have opposition. Actually, the science part isn't the prereq, it is the "advocate for public policy changes". Lots of groups who advocate for public policy changes get villianized. It sucks, but it should not come as surprise to anyone who enters into that arena. If you (generic) want to be left alone, keep your head low. If you (generic) want to stand up for something -- you will be opposed.

REACT:
C. Educate. In my opinion, the scientist is supposed to educate people in a simple a terms as possible. I believe scientists used to view this as part of their duty and I believe it has been something that has been generally lost (fwiw I have a 3 volume set of articles that great scientists such as Einstein and Bohr wrote for lay people that span over two centuries... often the articles were published in newspapers.. I have loaned it out, otherwise, I'd list the set for those interested). To educate the lay people, write articles for news papers or online venues. Engage critics with openness, because in doing so professionalism is shown and confidence is built up.

D. Be respectful. Don't refer to people who disagree as deniers or anti-science or ignorant. Give them the benefit of the doubt. Figure out the faulty metaphors they are employing and reveal them. At the worst, agree to disagree. I have recently encountered a scientist doing exactly this, and have been very impressed with him (and I expect I disagree with him on some fundamental beliefs), but I have contacted him to encourage him in what he is doing, and even sought his feedback on some of my own interests.. because I can trust him to be methodical AND respectful. Respect opens up the possibility for long term dialogue. Also, keep in mind that your audience isn't only the person asking questions or postulating absurd theories. It includes the people who are undecided watching the debate (or reading the news article, etc..) as well as the minority / subset of the opposing view who are willing to listen.

FOLLOW UP:
E. Make a point of gathering objections, alternative theories etc, and having the data that refutes them readily and publicly available. This is just a tactical confidence building move.

SUMMARY:
Please note, I'm not encouraging necessarily that a single person do all these things. Happily scientists do not work alone, are part of associations, etc.. and collectively they can do these steps and maintain/gain/improve a good footing with the public. And doing so in a respectful way will gain more good will (even from people who disagree) than you might imagine.