There could be a mixture of reasons for this. First, Scout is growing up. She is now at school and, although we don't see a lot of her there, this has presumably put a different structure and discipline in her life. Second, as the novel proceeds and events surrounding the Tom Robinsion trial begin to move centre stage, Calpurnia may soften towards the children through knowing what pressures are now entering their lives. It is true that this applies less to Scout than to Jem, who understands better what is going on, but Calpurnia is shrewd enough to see things from both the children's point of view and may ease off a little because of the trial. The visit to First Purchase may help too. However, I think the most likely reason is that Calpurnia has to fade into the background a little as the novel proceeds because her role naturally diminishes as the trial looms large. It's a little disappointing that such a strong and interesting character does fade - I always find her absence from the novel's ending disappointing even though she wouldn't naturally have been at the house at that time - but better that than keeping her to the fore artificially. Her presence at the Missionary Circle gathering is satisfying though, and it is here that she and Scout really come together on an equal footing - maybe a satisfying enough exit for Calpurnia after all.
I think the main reason for this is that actually, all the "meddling" and "unfair" etc. things Scout says Calpurnia has done are not half as bad as she makes them out to be. It is clear that Calpurnia loves Scout very much, and although she is sometimes strict, she is never in anyway unkind or unjust in her treatment of Scout, which tells us that Scout is exaggerating her meanness, as all children do about their figures of authority. A good example of this is when Scout calls Cal's presence "tyranical" because "she calls me when i'm not ready to come in". Although this is sound justification for a child, Scout probably would have missed her super had she not been called by Cal. However, as the book progresses and the children mature in attitude, Scout (albeit begrudgingly) realises that Calpurnia does mean well, as she sees how petty the apparantly mean things Cal does compared to the great prejudice of the other people around her, and as a result, stops exaggerating her strictness and dissproves generally, as although she won't admit it to the reader or anyone else, she has very little or no reason to think badly of her.