I don't think it's fair criticism of Pop for taking Bowen out with 3 fouls.
If up 20 points midway through the third quarter isn't a good time to save Bruce for the entire fourth quarter with an ample amount of fouls, when is? If the Spurs were up 30, would it be ok? If the Spurs were only up 2 points, would that have been more acceptable?
The decision is a catch-22. If Pop leaves Bruce in, and Bruce gets a foul the very next possession, Pop is forced to take him out and probably won't be questioned for taking him out at that point. But, say that happens and the Lakers still make their run and in the fourth quarter, Bruce fouls out with 2 minutes to go in the game and Lakers win by the same 3-4 points. Then, everyone and their mamas question why Pop didn't take Bowen out when he got his 3rd foul when the Spurs were up 20 points.
Catch-22.
Pop knew Kobe was going to get aggressive and the Lakers were going to make a run. What Pop was doing was playing the odds. The Spurs were up 20 points, Bruce was going to need a little bit of a rest anyway late in the third or early in the fourth. He gets extra rest and he can play basically the entire fourth quarter with 3 fouls to give.
It actually makes too much sense. But, it didn't work.
It's easy to question the decision in retrospect. Hindsight is 20/20. The decision may have been one of the reasons for the loss, but at the time, it wasn't a horrible decision if you think about the risk versus reward scenarios of leaving him in versus taking him.