While Carson McCullers does not directly say in The Ballad of the Sad Café why Miss Amelia rejects Marvin Macy after marrying him, we can infer that Marvin wanted to have sexual relations with Miss Amelia that she definitely did not desire.
No one quite knows why Miss Amelia married Marvin Macy when she was a young woman. Perhaps she was simply lonely, for her father was dead, and she had no one else. Perhaps she was impressed by Marvin Macy's attention and by the thought that his love for her had tamed this wild man. It took two years for Marvin to propose to Miss Amelia, and she accepted him.
Yet Miss Amelia's behavior after the wedding was strange indeed. She was definitely uncomfortable during the ceremony, and then she left the church ahead of Marvin and went directly back to the store and back to work. She didn't speak or act like she had just been married, and we can infer that Miss Amelia was probably regretting her marriage already.
Then that night, Marvin and Miss Amelia went upstairs to bed, but pretty quickly, Miss Amelia came right back down, angry as can be. Again, we can infer what happened. Marvin wanted to have marital relations; Miss Amelia clearly did not. Marvin did everything he could to try to make Miss Amelia join wholeheartedly in their marriage. He gave her presents. He signed over all he owned, but nothing worked. She slept in a different room.
One night, Marvin got drunk and tried again. Miss Amelia hauled off and hit him. A while later, she kicked him out. When he climbed through her window one night, she tried to send him to jail. After only ten days, Marvin left town, leaving Miss Amelia with all his possessions.