This topic is actually one of the issues discussed in the Geek Social Fallacies, but here's a nice easy example. Would tolerating planet posts encouraging the eradication of the Jewish population be inclusive or exclusive? I suspect that most people would agree that it wouldn't be acceptable behaviour, which leads us to the next question. Why? There's two obvious arguments here. The first is that at a community level we have some form of rough moral consensus that advocating genocide is Just Wrong, and so criticising Nazis is obviously the right thing to do. The second argument is more pragmatic than philosophical - alienating millions of people in order to avoid alienating hate groups could be considered to reduce our potential contributor base in an unfortunate way.
I'm a fan of the second argument. The example I gave is emotive and relatively recent history has resulted in people tending to be pretty uniform in considering genocide to be a bad thing, but many other cases aren't clear cut. What I consider to be objectification of women is seen by others as appreciation of natural beauty. What I think of as sexist jokes are perceived by others as acceptable humour. When I advocate intolerance of certain behaviour, people are going to see me not having enough tolerance. So we end up in a situation where people make the "We should all just get along and be tolerant of each other" argument, which sounds fine but is fundamentally flawed in one significant way.
Advocating tolerance excludes the intolerant.
The reason people fail to see this is that it doesn't sound like a flaw. If you ask people whether we need to support intolerance, the immediate answer is probably no. But by advocating exclusion of intolerance, you're excluding all those who have good reasons to be intolerant. You're excluding the women who don't want to feel that the community sees them as a pair of breasts attached to some legs. You're excluding the ethnic groups who would prefer to avoid racist slurs or ethnic stereotyping. Telling anti-fascism protestors that they're being intolerant isn't likely to endear you to them. Advocating tolerance is telling the intolerant that they're wrong and should just deal with whatever it is that makes them unhappy.
So, ironically, tolerating certain types of intolerance is probably required in order to avoid alienating many potential contributors. That means some way of deciding what kinds of behaviour are acceptable and which are unacceptable. In the absence of either pre-existing community consensus or some philosophical breakthrough that allows unambiguous determination of the "rightness" of a given action, I'm going to suggest that we look at it from a pragmatic viewpoint. How many potential contributors do we discourage by criticising a certain type of behaviour? How many do we discourage by tolerating it?
The fallacy of the completely inclusive community is the idea that it includes everyone. The reality is that a certain level of social exclusion is required in order to include a wider range of people. So don't criticise people purely for criticising someone else's behaviour - make an argument for why that behaviour benefits the community. And when you see behaviour that you think discourages others, call people on it. Even if nobody's behaviour changes as a result, you're sending a signal that not everyone in the community agrees. Sometimes all people want is to know that there'll be some people on their side.
But, above all, try not to be a dick.