Nadal would have played on no matter what but he made a bad motion on a dropper at the end of the second set. Read his presser,he tells how it happened. You really think it would have been humiliating for Nadal to be breadsticked or bageled in a slam after what he's been through since may last year(including triple 6-2 in USO)?
If Nadal had a reputation as a quitter maybe I would see it but as it is I believe Nadal. If he had somehow won the second set while having problems after the dropper he would have been in a real pickle. Rafa is tempestuous,pushed himself like a madman and I think he would have tried to bear and grin it,no matter how much it hurt(but he couldn't have possibly won because he couldn't move well off his fh side) but there is absolutely no way the adrenaline would have lasted five sets. He would have quit at one point either way.
Basically it boils down to this: Nadal saw that the old pain was back(the one that made him skip WB) and after the trainer session gave it a go and,unlike the nadal of old,decided not to go all the way. The memory of what happened to him in 09' was reason enough to make him want to quit,especially after he saw that he couldn't move properly in the third. Did the fact that he was 2-0 down play a part? Probably but not that much. Let's say Rafa was leading 2-0 and he would get pain in the knee. He could probably squeeze out a set but no more. And trust me he would need a pretty bad opponent because he would need to get a set off him on one leg.
Rafa and Andy know each other since they were 13 and Andy looks up to Rafa because they are almost the same age yet Rafa has matured before Andy. The thing Rafa did in Rotterdam was very gentleman like(though it was probably stupid in retrospect),staying a whole set on court despite having problems,just to give murray a clean win. He was probably feeling generous after AO. In 2010 Nadal is starting to take care of himself,at least that's what I hope.