but the bigger issue wasn't Dirk scoring points as much as it was Timmy getting rung up with fouls
Which he was.
and: (1) ending up on the bench because of foul trouble;
Which he did.
(2) ending up playing passively because of foul trouble;
Remember that lame charge he tried to draw against Dirk one on one?
(3) ending up gassed from having to chase all over the floor;
Having to rely on Horry and Finley as your shot blockers meant Timmy had to patrol the lane by himself, at least when Horry and Finley weren't screening him.
Pop couldn't ask Tim to defend Dirk for 42-44 minutes every night --as great a defender as Timmy is, that's not his defensive game.
Yet he could ask Duncan to be the only offensive weapon and the only hope of stopping the entire Mavericks team when they got into the paint again and again and again. Tim Duncan is one of the top defenders in the league every single year. And oh by the way, he also has a teammate who is one of the top defenders in the league, so he wouldn't have been defending Dirk for nearly that long a stretch. Defense was not going to be the Spurs' weak point going into that series if they played it the way they knew it with the people that were on the team for that purpose. Dallas has had better offensive teams in the past, and the Suns from the previous year was even better, and the Spurs didn't scrap their defensive mentality, and they won. You can make stupid little jokes about what a terrible shot blocker Rasho was, but he was light years ahead of Horry or Finley, and he played good team defense. Funny that people that never appreciated it when it was there don't understand why the Spurs got burned so bad once it was gone.

Had Pop stayed big, it his choices were to run Timmy at Dirk, run one of Rasho/Nazr at Dirk, or put Bowen on Dirk and create a mismatch elsewhere on the floor. Given those options, how exactly was Pop supposed to keep Rasho or Nazr on the floor without seriously jeopardizing the Spurs' chances to win? Seriously.
All three of those options would have worked. All three of those options were better than ending up with Devin Harris and Jason Terry going past their defenders only to score on Horry and Finley for the entire game. Did it occur to you or to Popovich that all three of the above that you mentioned can be thrown at a team at different times which disrupts their offensive flow? That's what defensive minded teams do to good offensive players. Instead the Spurs allowed the Mavericks to play within their comfort level for the entire series because they trotted out a team that couldn't do what they were good at because they were too busy trying to make up for the handicap placed on them by their coaching staff.

If only it were that easy. If you put a tall guy in the rotation to just stnad there and be tall, again, you're sending your best rebounder out on the floor and asking him to take on a defensive mismatch while working him down to the point that he likely wouldn't have been as effective offensively. Do you really think that would have been a good idea?
Again, I only have years of success by the Spurs and 63 regular season wins to fall back on. When your philosophy is to funnel dribblers to the shot blockers and then you suddenly put your two worst defenders in there as shot blockers, I'm curious as to why you don't question if Pop had money on the ing Mavericks. Duncan did more chasing in the paint and had more bad fouls because Rasho and Nazr weren't there.

Great. And where are you going to get offense when they're in foul trouble along with Tim Duncan?
Tim Duncan was in foul trouble during the series. What are you saving Nazr and Rasho's fouls for? Can they use them on their new teams?