Ok, I'm gonna try to break down what's happening on my site.
User A is friends with User B and User C. User B leaves a comment on User C's wall. User A receives a notification of this content in his feed.
I don't think User A should receive a notification of this, because it's a direct (albeit public) communication between Users B and C.
Which of these notification settings (if any) controls this particular type of notification? I would like to default disable the one that is causing this.
This is how fb does it too. I'll go check activity feed settings as it might be there.
Experiment with admin/activity/settings/types/plugin/user and see if setting that last one to uncheck Main Feed would work for the option of when a member comments on another member's wall. This would stop it from showing for both of them though in the main feed but that user c would still get notifications and see it on their own wall.