Strictly speaking, what changed was, not the atmosphere, but the procedures. The Apollo continued to use pure O2 after the Apollo 1 fire; to redesign for a two-gas system would have set back the program substantially, and caused a ballooning of the vehicle's weight. What was done was modification of the launch procedures. On the pad the atmosphere in the cabin was changed to "breathing air", drawn in from outside and purified by ground support equipment. After launch, a system of valving gradually changed the atmosphere over to pure O2 as the vehicle climbed and outside pressure dropped.

-Kim-
Pad rat, KSC