Maybe the moderators would consider a Science Caucus. No scientific topic can be discussed in Free Republic without it devolving into this kind of squabble. There is no basis in trust, of philosophy, or even a common fact base for productive conversation to go on so I think it would just be best for everyone concerned to separate the two sides with a caucus barrier.
I usually stay out of the creation/evolution debates. The last time I jumped into one was just to point out that I really dislike the mischaracterizing of scientists as lunatics trying to foist off some new-age style beliefs in the guise of science, and got drawn far more into the discussion than I really would like.
This thread, however, does not seem to be posted as a creation/evolution thread, but was talking about the science itself. And I'll never hesitate to jump into a discussion about science. In this case, it's the non-scientists jumping in that started a debate. Most of the scientific threads posted on FR do not, in fact, end up as debates.
I second your idea! These threads get so ugly that it is almost painful to read them.