Reputations form the basis of the emotional bonds that form the community, and the desire to bond emotionally drives the creation of reputation. One shouldn't underestimate the power of emotional bonds; super-strengthening these bonds will give the best chance of protecting the reputation system.
Therefore, to ensure that contributors maintain a reputation and respect the reputation system, RewardReputation. Reinforce the emotional investment. After a person has put so much time and effort and love into building herself within the community, and after she has gained so much respect and admiration and trust from the community, she is unlikely to just abandon that identity or attempt to create an entirely new one from scratch.
But, of course, the more emotion invested, the higher the stakes, and the higher the risk. A community's greatest threat is not some random attacker, but a member of its innermost circle. This is why the opposite of RewardReputation is not PunishReputation.
Moreover, some people are just beyond all social protocol. They might be alexithymic, sociopathic, schizoid, or any number of neuroses or disorders. Some are just troublemakers, or trolls (cf. WhatIsaTroll). For these, we DissuadeReputation.
First, offer privileges that only work with identity, such as a MessageBox or a FrontLawn. Don't underestimate ego investment. Second, and more importantly, invest more emotion in people as they invest more emotion in the community. Give positive feedback.
This can be as simple as thanking people as they contribute. One can personally greet people who introduce themselves, as the MeatballWiki community does with the CategoryHomePage tradition. Public AwardRituals can be given to people who do exceptional things, and they form a PublicMonument? to point others to good RoleModels; for example, the BarnStar award.
It's also common to give people more power the more they contribute. OpenSource projects typically only give commit access to the most valuable developers in the community. LambdaMoo created a hierarchy of wizards to administrate the site. WikiPedia gives away system operator privileges to the most trusted members.
Sites that track reputation more quantifiably often give privileges automatically as members' reputation "scores" reach certain threshholds. KuroshinMojo is an example, whereby a high Mojo score yields the power to rate comments as zero. SlashDot gives its users +1 rating bonuses if they receive enough positive feedback from moderators.
However, take care not to give material rewards automatically or by some fixed scheme. These cheapen the relationship by equating an emotional investment to an unemotional return. Moreover, SlashDot's KarmaWhores should provide enough warning about the consequences of giving material rewards automatically. The reputation system can quickly turn into a game that some in the membership, already jaded by the cheapness of material rewards, will most likely exploit just to annoy you.
Worse, if gaining privileges become a competition, some people might resort to "underhanded" (read: unexpected) methods to win. If the competition is too hard, people will give up, and then they will no longer care about the repurcussions of their actions, making them disruptive. If the privileges are too valuable, people will become envious, which may create tension (a notable antipode is KuroshinMojo, where "trusted moderator" status is an undesirable burden, not a privilege). Thus, it's best to keep rewards within the social realm of respect and trust.
A classic example of the downsides of automatic reputation tracking is UltimaOnline?. Every player-character has an alignment (ranging from demonic to saintly) and a fame (ranging from nobody to world-famous), both of which are tracked automatically. One gets an evil alignment by attacking people without provocation, for example. The system is pretty complicated, with some non-obvious consequences. For example, you're in the middle of the wilderness, practicing your area-effect spells. A nasty player deliberately moves into the area-effect - this means that the game believes you've launched an unprovoked attack on them. The nasty player then kills you, which the game believes is legitimate revenge. Consequences: your alignment becomes more evil, while the opposing player's alignment is unaffected, but they become more famous.