Good point, opher.
I think that the point of when to take a fall or not must include both making sure that you and nage are learning and that you are staying safe. You don't want to resist a technique just because as that can lead to serious injury.
Ledyard Sensei has a great article on Appropriate Ukemi
that you might also want to check out. I found it very good and it might be helpful for you in relation to this question.