IMO...when it comes to exercise/physical conditioning...if you are not confronting the mental aspect of pushing through the pain, you are missing out on 85% of the benefit of the training.
I'm talking about the "this hurts I want to quit" mental aspect of conditioning, not "I think I tore a tendon" or "I'm significantly damaging myself" pain. There is a big difference.
I just completed a 17 mile in one day "hump" through mountainous terrain (including summiting a peak) . I did it for both physical and mental development. While the physical training aspect was undeniable, the most benefit I received from it is that I know I can override my brains messages to "give up!" and just keep on going. Of course I have military experience and knew that I already had some stress-inoculation on the topic, but I like to see if I still "have it" on occasion.
There is a portion of martial arts training that should exist, which is the struggle. Pushing through the struggle is part of the development of self-discipline that so many of us gain from MA. If we can devise exercises that combine a planned struggle with something else (fitness development, practicing technique, etc.), then so much the better.