Many sites have issues with users abusing comments to violate the be nice policy. Currently other than the occasional warning or suspension there is no real deterrent. The lack of any noticeable penalty, I suspect, fuels the willingness of these users to engage in the disruptive behavior that Mods are forced to deal with.
If a comment is removed for being rude or abusive, a penalty of 25 rep being applied would be a good reminder that this behavior is not acceptable, and provide a tangible penalty for misbehavior. In addition if these changes were visible to other users, they might choose not to engage in comment banter with someone who has a track record of disruptive comments. In the end both of these results are a win for both moderators and the community.
This would also have a positive effect for Hot Network Questions where users not normally engaged with the community, have the ability to comment snark and engage in disruptive comment behavior. Just a few instances of misbehavior in this manner would see their ability to comment revoked until such time as they provide a positive contribution to the community.