Conflict is good when managed and it adds value. You usually end up with more rounded or more complete ideas. This can fail when there is a lack of respect between adversaries, a lack of understanding or a lack of truth from at least one side.
On your point of community vigilance, Administrators/site owners should set the rules of engagement and a culture (eg. No ad hominem attacks). If the community determines the rules of engagement, you can have the community derail itself far too easily. I'm seeing quite a few communities lose the plot recently through political correctness or through a hostile community that self-regulates. One of the best sites I visit is very rule based. The moderators do a great job of setting the rules and when the community loses focus, the site owner/moderators recalibrate. I keep thinking of leaders vs committees as a good parallel.
I don't have simple rules about what rules should be applied to respect in conflict. There are several examples of exceptions that come to mind: Karl Popper talks about not tolerating the intolerant; Political Correctness can introduce prejudice (and has spoilt some good communities).