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 to bright and well-spoken community members and high-visibility dissonant posts belonging to trolls or random crackpots (who in turn have incentives to ignore those same chilling effects).
Without getting rid of the karma system entirely, one possible defense against this sort of effect might be to encourage a community norm of devil's advocacy. I see some possible coordination problems with that, though.
If the community norms are ones we don't endorse, then sure, let's overthrow those norms and replace them with norms we do endorse, in a targeted way. Which norms are we talking about, and what ought we replace them with?
Conversely, if we're talking about all norms... that is, if we're suggesting either that we endorse no norms at all, or that we somehow endorse a norm while at the same time avoiding discouraging contributions that violate that norm... I'm not sure that even makes sense. How is the result of that, even if we were successful, different from any other web forum?
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.