I think you answered the question yourself: you shouldn't be doing anything at the expense of health. In regards to lowering the bar onto your shoulders, it has it's place and is very useful (for reasons you already mentioned).
In my opinion, the best way to approach this is to go by feel. If you've identified your shoulders as a weakness, then I don't think you're overtraining if you're executing the outlined plan. You're overtraining if you neglect to deload every once in a while and continue to increase the loads on a weekly basis. Some days, 70% is going to feel like 90% and 90% will feel like 70%. These are just things you have to listen to your body for in order to adjust your training in terms of load and volume, and whether you lower the bar onto your shoulders or blocks.
Hope this helps,
Javier A. Sanjuan
Olympus Barbell Club
Dear God, please help me lift heavy and be awesome. Thanks. Amen.