You're correct that you should take care of your partners in training. They should also take of themselves as well though. It's a two way process.
So in the scenario described by the OP, he probably should not have pulled his partner if his knees were in an awkward position. Likewise, his partner should also be less worried about complaining and more worried about not putting himself in such a dangerous position in the first place.
It's like when I sweep people over my head. If they stick their head out stupidly, I will not sweep them hard onto their face and hurt their neck. I will ease up and take it to the side instead for safety. However, I also let them know that they need to be careful with that and should tuck into a roll instead when I have that sweep.
Good safety involves protecting your training partners and teaching them how to protect themselves too.
Total agreement.