Is that really an issue? If the user makes more uncivil comments then you flag them again until they get the picture. There are plenty of other places on the internet that seem to welcome and encourage flame wars -- they can go there to work out their resentment and then come back when they're ready.
If something disappears, no one has bad feelings about it.
If something two people are arguing over disappears, then two people carry simmering resentment about it (ironically, likely more than if their verbal spat had reached a cathartic conclusion), that eventually manifests in their next comments, and which ultimately leads to an erosion of common decency and civility.
It's a fine line, but it's definitely a line rather than right vs wrong.