I can tell you from experience, that it really depends a lot on who finds things like your .30-06 pen, and who the Supervisor at that time is, as to whether you'll get to keep it or not. One of TSA's biggest criticism's was inconsistency between airports. Most people didn't realize that it was really inconsistency between screeners and supervisors.
I'll tell you that things like that pen aren't really a grey area, but there are people out there who make them a grey area. Unfortunately, you probably did the right thing (if you wanted to avoid getting hassled about it, anyway) by throwing it away.