Is there as much of a problem with the karma system as you make it out to be? I've posted comments critical of cryonics, comments critical of the idea of hard take off being likely, comments critical of Eliezer's writing style, and comments critical of general LW understanding of history of science. Almost every such comment has been voted up(and I can point to individual comments in all those categories that have been voted up).
I suspect that quality threshold for critical comments being voted up is higher than that for non-critical comments, and that the threshold is similarly more strict for low quality comments being likely to be voted down. But, that's a common problem, and in any event, high quality comments aren't often voted down. So, I fail to see how anyone would be substantially discouraged from posting critical comments unless they just weren't very familiar with the system here.
It seems to me that the karma system needn't foster any actual intolerance for dissent among voters for it to have a chilling effect on dissenting newcomers. If a skeptical newcomer encounters the site, reads a few dozen posts, and notices that posts concordant with community norms tend to get upvoted, while dissonant ones tend to get downvoted, then from that observer's perspective the evidence indicates that voicing their skepticism would be taken poorly -- even if in actuality the voting effects are caused by high-visibility concordant posts belonging ...
You see, I've seen the word "rationalism" used to mean all five of these things at different times:
Edited to reinstate that proposed solution, since this discussion is presumably finished.