Let's not forget that Josh Smith got hurt in the second half and that Hollins fouled out rather early in that second half as well, causing Larry Drew to go to an extremely small lineup through most of the third and all of the fourth.
Most of the third and fourth quarters the Hawks went with Ivan Johnson at center and Marvins Williams at PF. Doc knows Williams can't guard Pierce so he moved Pierce to PF, and in order to battle the taller wings the Hawks have(Johnson, Hinrich, McGrady) Doc countered with Q and Pietrus. Remember Pietrus was rested from not having played almost the entire first half because the refs rang him up for 3 fouls in the first 4 minutes.
So Bass sat and Stiemsma sat and given the results, it seems to have been the right move. Simply put, Doc believes his small ball lineup is way better than their small ball lineup and I would have to agree with him.