I'm not a doctor and I certainly have no inside knowledge of Nadal's injuries, but this is how I think of them:
If you were given the wish to win a Slam tournament, with the condition that every shot you made, you were hit in the shin with a hammer (it didn't slow you down or hurt your performance, but you experienced a lot of pain) would you do it? Certainly, many of us would choose to do that. However, after the third, or fifth, or eighth, slam title would the pain be worth it to you? Maybe you just would be sick of it and not so excited to go out there again.
Maybe playing just on clay where it wouldn't hurt as bad might be OK with you after a while.