You can maintain the proper scapular position if you have the proper strength/endurance in the needed musculature, even if you go to a "dead hang". During the dead hang, you do want full shoulder flexion and elbow extension to occur. I hope I don't confuse this more with this but you are going to have SOME level of upward rotation during eccentric phase of the pull up in order to achieve full shoulder flexion. That being said, you DO NOT just want to disengage your lower traps, rhomboids, and other scap retractors/depressors. Think of it this way, you can be at the bottom of the pullup in one of two ways:
1) You disengage the scap retractors/depressors and just let your scap fully rotate upward and you completely hang then with your GH joint in a biomechanically weaker position and primed for shoulder pain/injury.
2) You maintain scap retractor/depressor activation, allow the proper and needed amount of upward rotation to reach full shoulder flexion (or at least 180 degrees), and maintain the proper joint positioning.
Both examples show a "dead hang", but one is much more beneficial than the other.
Great advice here. Generally the smaller muscles that are involve in scap retraction/depression (lower and middle traps, rhomboids, etc) are weak/inhibited. People try to compensate for that with more gross pulling exercises (rows, pullups, etc) but majority of people get caught up in the weight being used or the number of reps being done and do not focus on targeting the correct musculature.
I would recommend starting with some scap retraction/depression activation drills (wall slides, band pull aparts, etc) and then progress to a strengthening based exercise for those smaller muscles, and then progress with pull ups. As Shadow said, you may need to cut back on your pull up reps as I doubt you are keeping the proper scap position during your whole set.
Here is a great article by Mike Robertson on lower trap training which you should find helpful: http://www.T-Nation.com/free_online_article/sports_body_training_performance/top_priority_for_lower_traps
Again think of pulling your scapula into your back pockets at least during all pulling exercises and benching.