You are correct that the speaker is censuring someone for running away.
However, it is not correct to characterize the phrase "Run away from me" as an imperative. The sentence is a question and that phrase is actually simply part of the question. What makes it difficult to understand is that the sentence contains two inversions.
An inversion is a sentence structure in which the usual word order is reversed. The usual word order is “subject” followed by “verb.” An inversion places the verb, or part of the verb, ahead of the subject.
The two main reasons for inversions are (a) to ask a question or (b) for stylistic reasons. The sentence you are asking about has both types of inversion.
The verb in this sentence is "will run." The normal word order is "You will run."
The first inversion is the placement of “will” before “you.” In this inversion the helping verb ("will") comes before the subject; this is a normal word placement for a question.
The second inversion is the placement of “will you” at the end, after “run away from me.” The second inversion is done to set a tone, and for emphasis.
If we undo that inversion, the sentence reads: “Will you run away from me?”
This re-ordered sentence clearly is a question. However, it does not have the same angry undertones as the original, inverted sentence. The inversion places emphasis on the act of running away and in the context adds meaning without words.
As it is stated in the “Inversion” tutorial provided by Learn-English-Today.com
Inversion . . . is a literary technique in which the normal order of words is reversed, generally for emphasis or special effect. It makes a sentence sound striking or unusual. It also sounds quite formal. Sentences with inversion are less common in ordinary English. In a sentence with no special effect or emphasis, the normal order of words is retained.
Example 1: I have never seen such a beautiful rose.
Example 2: Never have I seen such a beautiful rose.
For more information about inversions, you may wish to start by taking a look at that tutorial. http://www.learn-english-today.com/lessons/lesson_cont/verbs/inversion.html