I would argue that this excellent coming-of-age short story is actually centred around an internal conflict within Elena herself, and the gap between her dreams and hopes and the brute reality that she has to face because of her ethnicity. This of course also is manifested in the external conflict in the way in which Eugene's mother treats Elena when she goes to his house, and is foreshadowed by the way in which Elena's mother warns her daughter about what she is heading towards:
You are forgetting who you are, Nina. I have seen you staring down at that boy's house. You are heading for humiliation and pain.
Thus it is that Elena's conflict is between the hopes that she has for herself and her friendship with Eugene and her ethnicity and the way that it makes her different from others. The death of her hopes is of course paralleled with the death of JFK, who himself tried to campaign for equality.
Additionally, the main conflict can also be placed in the character-versus-society category.
As the story progresses, we come to the realization that Elena feels alienated from her parents, her school peers, and mainstream society. First, she is Puerto Rican, and her command of English isn't good enough for her to be admitted into honors classes at school. Elena also finds herself rejected and ridiculed by the African-American girls she tries to best in rope-jumping. Because she is thin and small-framed, Elena finds it difficult to keep up with her more robust peers. Her schoolmates cruelly refer to her as Skinny Bones. As a small-chested Puerto Rican teenager, Elena feels self-conscious and humiliated that she lacks the kind of physique the more popular girls have.
Elena spends much of her time at home reading on the fire escape in her apartment building and spying on an older Jewish couple in the house next door. Eventually, the husband dies, and his elderly wife moves out. A new family moves in, and there is a teenage son in the mix. Elena finds herself falling in love as she watches Eugene. However, her mother is unsympathetic when she discovers Elena is interested in the boy next door. She unceremoniously tells Elena that she is just love-sick or "stupidly infatuated." There is not much positive interaction between the mother and daughter; instead, Elena has to endure her mother's incessant warnings about the need to protect her "virtue" and "morality."
Elena is drawn to the novel Gone With The Wind because it tells the story of a beautiful heroine (who has devoted parents to support her and slaves to serve her). When Eugene invites her over, she is over the moon. However, Elena receives a rude awakening when she knocks on the door at Eugene's home. Instead of Eugene, she is greeted by his mother.
Eugene's mother unequivocally rejects the idea of her and Eugene studying together. She curtly tells Elena that Eugene is a smart boy and that he doesn't need Elena to study with him. Basically, Eugene's mother doesn't want her son associating with a Puerto Rican girl. Shocked at the woman's rudeness, Elena makes her way home. However, she receives no comfort or solace there. President Kennedy's death has shocked her parents, and they are in mourning. So, Elena must comfort herself as best she can in her bedroom.
From the above, we can see that the overriding conflict in the story rests in the difficulties Elena must face in navigating the society she lives in.