I would have to say that I have no problem with a family member holding a spot in the checkin line. I've done this many times myself as well. What is frustrating is why folks insist upon starting the line as much a 1 1/2 hours before departure time. It just makes no sense, and once a few people get in line, everybody does.
As a Companion Pass holder, I would also appreciate being able to pre-board. However, I don't see this as very likely to happen with Southwest's business model. They are at least beginning to crack down on 6 people pre-boarding with one child. Thanks for that!
In all the years I've been flying Southwest I have not noticed them holding back the first boarding passes for through passengers. The gate agent knows the exact count of throughs and they will process and give boarding passes only to the correct number of originating passengers. Remember, not all 737 aircraft hold the same number of passengers.