This is a very poignant question given the Naturalistic perspective by which the story was written. Typical Naturalistic pieces exemplified the importance of "man as a beast", or animalistic behavior by man. Therefore, your question poses one which can be looked at as simplistic or theoretical.
To begin, let us look at the simplistic answer to your question. Many would argue that old woman Magoun is by far the biggest beast in Freeman's story "Old Woman Magoun". There are many reason as to why one would consider her behavior beastly.
First, Magoun keeps Lily, her granddaughter under lock and key. To say that Lily is sheltered is an understatement. The one time in which Magoun allows Lily to leave on her own is the turning point of the story (she meets her father Nelson Barry for the first time on her life). Lily's life, and that of Magoun, is changed forever.
Second, the fact that Lily is sheltered pales to the fact that she remains childlike in her appearance and actions (Lily still, at almost 14, plays with dolls). Lily is described through a conversation of Magoun and a friend of Magoun's (Sally Jinks) in the following way:
“Some girls at her age is thinkin' about beaux instead of rag dolls” said Sally Jinks.
The grandmother bristled. “Lily ain't big nor old for her age,” said she. “I ain't in any hurry to have her git married. She ain't none too strong.”
“She's got a good colour,” said Sally Jinks. She was crocheting white cotton lace, making her thick fingers fly. She really knew how to do scarcely anything except to crochet that coarse lace; somehow her heavy brain or her fingers had mastered that.
“I know she's got a beautiful colour,” replied Old Woman Magoun, with an odd mixture of pride and anxiety, “but it comes an' goes.”
“I've heard that was a bad sign,” remarked Sally Jinks, loosening some thread from her spool.
One can tell from this conversation that Lily is not necessarily healthy. This, again, can be contributed to the care that Magoun takes in the girl.
Lastly, and perhaps the most poignant example of Magoun's beastliness is the fact that she poisons Lily. Magoun cannot bear to think of Lily living a life with her father and believes that death would be better for Lily.
Now, onto the more theoretical answer to the question. Naturalists believed in the power of nature over man. Nature "decided" the outcome of all which happened in life. Therefore, one could justify an argument that Nature (used capitalized because of personification typical in the movement's texts) is the "biggest beast" in the story "Old Woman Magoun".
Nature is not concerned with anything. It simply exists and what happens as a result of Nature's powers is simply because of the theory of the survival of the fittest (Charles Darwin and Herbert Spenser greatly influenced Naturalistic writers). That being said, one could interpret the "cruelty" of Nature in allowing a young girl to die as representing the grandest beast in the text.
It is not Magoun who takes the life of young Lily; it is, rather, the nightshade berry. Magoun did not create the berry- Nature did. Magoun even, earlier in the story, told Lily that she could not have the berries. (Although her exact words were "You can't have any now.")
So, depending on your school of thought, either Magoun or Nature can be defined as the "biggest beast" in the story "Old Woman Magoun".