Chapter five, of Mary Shelley's Frankenstein, proves to be a great turning point in the life of Victor Frankenstein. Up until this chapter, Victor devoted much of his life to re-animation and science. After this chapter, he spent the remainder of his life trying to destroy what he had spent years upon.
Given this question poses a very subjective answer (readers will vary on their responses), this summary will provide both sides of the prospective argument. That said, some background from chapter four is necessary.
In chapter four, Victor (through Walton's retelling) speaks about the trials and tribulations he faces in creating his "son." The work he performs is both difficult and laborious. Readers find him reveling in how his "son" will react towards him.
A new species would bless me as its creator and source; many happy and excellent natures would owe their being to me. No father could claim the gratitude of his child so completely as I should deserve theirs.
Victor places himself on the level of a god. Given this position, his possible fall will be great.
Given the great lengths Victor goes through to work the delicate muscles, fibers, and veins, he takes great pride in his work. The "pieces" he chooses was done so with their beauty in mind. He desires nothing more than to create a beautiful being who will owe its life and gratitude to Victor.
Therefore, upon the re-animation of the "being," Victor's actions can be understandable. He has toiled so hard that the "catastrophe" laying and convulsing in front of him proves to be far too overwhelming. The years he has spent constructing his "son" are in vain; the being disappoints him far too greatly. He possesses so much fear at what lay before him that he can not face either the being or what he has done. He has no choice but to flee.
On the other hand, Victor could accept what he has created. He has toiled for so long that one would expect him to embrace his "son," regardless of what he may look like on the exterior. This being depends upon the loving embrace of his creator; he depends upon him for love, support, attention, and education.
Therefore, the choice to support or disagree with Victor's running from the Creature lies in one's understanding of unconditional love or disappointment. One can easily argue that Victor fails to possess the nurturing love of a mother (given typically it is the mother who births the child). On the other hand, one can (just as easily) support his failure to embrace his son based upon the outcome of his birth and physical appearance. Either way, a strong argument can be made either in support or disagreement of Victor's choice to abandon his son.