The body in Emily's room is not her father's body. The body is presumed to be that of Homer Barron, the man Emily had a brief affair with.
Soon after Emily is buried, several of the men force the upstairs open. There they find what is evidently the rotten corpse of Homer Barron. Even more grotesque, they find a long strand of iron-gray hair on the pillow next to his remains.
The gray hair found on the pillow presumably belonged to Emily and suggests that she slept or laid down next to the corpse.
Emily's reasons for keeping body in the bed have to be surmised/inferred. This open-ended aspect of the story is one of its most striking features.
...the real story lies not in the facts of the death; the true literary detective work comes with respect to uncovering the motives behind Miss Emily’s actions. (eNotes)
Emily may have been insane or may have been in a state of grief (either over the loss of her youth and her culture or over the act of murder). Her reasons for keeping the body are not explicitly stated in the text. The reader has to decide the answer to the question "why?"
What seems clear is that Emily committed murder, killing Homer Barron, and was able to continue on with her life. She also managed to keep her servants from telling anyone about the body upstairs, though the smell was so bad at times that the neighbors complained.