After making the obligatory "you need compliance initially to learn the moves" caveat, we tackle this in two main ways.
1. We practice with 3 levels of uke resistance when practicing the standard moves - basic, awkward and stubborn.
2. For free practice and randori - if you don't feel the technique/atemi is being applied, see if it is... ok, so this one occasionally hurts
but even then it's a valuable lesson for uke.
There's been several threads on this and someone (I think one of the Peters) gave an excellent pithy phrase regarding technique/resistance, but in my opinion this and all the "does it work" threads boil down to "can you afford to take the damage from training". If you can, then you can train bad habits out of people, if you can't, then you won't.