Does Holling change his feelings about Mrs. Baker by the end of The Wednesday Wars?
Yes. When Holling realises he is going to have a special one-to-one session with Mrs. Baker every Wednesday afternoon, he comes to the conclusion very quickly that Mrs. Baker hates him, and that in addition, she manages to induce in him a kind of fear that makes him want to vomit. Note how Holling responds when he realises how deep Mrs. Baker's loathing of him is:
...I felt the way you feel just before you throw up.
However, through the events that transpire throughout the book, Holling dramatically changes in his feelings towards Mrs. Baker, and comes to look forward to his Wednesday sessions rather than dread them. By the end he sees Mrs. Baker as somebody who has had an incredibly formative impact on his life, and whom he greatly admires and respects. Note the way that towards the end of the book, Mrs. Baker is reported as smiling, but with "not a teacher smile." He even begins to pray for her husband's safe return, which shows how much his feelings about her have changed:
I prayed for Lieutenant Baker, missing in action somewhere in the jungles of Vietnam near Khesanh.
Holling has realised that relationships rarely remain stable and that they may, indeed, change beyond our wildest imaginings. Mrs. Baker, starting the novel as his most terrifying person, slowly but surely becomes an incredible influence on his life.