Imagine a thousand professional philosophers would join lesswrong, or worse, a thousand creationists.

This test seems rather unfair--it's pretty much a known that people who join LessWrong are likely to be already sympathetic to the LessWrong's way of thinking. Besides, the only way to avoid a situation where thousands of dissidents joining could wreck the system is to have centralized power, i.e., more traditional moderation, which I think we were hoping to avoid for exactly the types of reasons that are being brought up here (politics, etc.).

The availability of a reputation system also discourages people to actually explain themselves by being able to let off steam or ignore cognitive dissonance by downvoting someone with a single mouse click.

True, but I think you have missed a positive incentive for response that is created by the reputation system in addition to the negative ones--a post/comment with a bad argument or worse creates an opportunity to win karma by writing a clear refutation, and I frequently see such responses being highly upvoted.

The initial population of a community might have been biased about something and the reputation system might provide a positive incentive to keep the bias and a negative incentive for those who disagree.

This is a problem, but based purely on my subjective experience it seems that people are more than willing to upvote posts that try to shatter a conventional LessWrong belief, and do so with good argumentation.