I think there may be an over reliance on pain in general in aikido technique as it is often performed. A proper joint lock controls the center...pain is incidental. If you rely on pain to make technique work, check to see if
A) Uke is unbalanced at the moment of contact
B) If using a joint lock, make sure you lock all joints leading to the shoulder, and from there lock the center.
C) practise doing the locking without inflicting pain. When properly done, uke should be controled...pain or no pain.
As for atemi and the reluctant uke...a slow, focused atemi that forces uke to move or block does wonders. You don't have to actually hit them...just place the strike and then continue to focus and push through the target. They'll usually move or block. You must make them feel your "intent".