Interestingly, I do not consider myself prone to genocide (I'm not a fan, not even in a mild way) and yet, I can think of people that I would love to see removed from the society I live in.
I think there are two things that may rub people the wrong way in that question.
1) The (over) use of the word hate. In English, hatred is almost always used as a hyperbole: someone who hates cauliflower probably does not spend his days thinking about destroying every last cauliflower in the world.
When hate is used without the (obvious) hyperbole, it conveys a very, very strong emotion, or rather, passion. A destructive passion at that. For that reason, hatred towards people is not often expressed outside emotional outbursts.
This is however not always the case for non-native speakers. I have noticed that many of them tend to use hate quite easily in situations where a native speakers would prefer dislike.
2) The fact that the hatred (or possibly dislike) is aimed at people, and not at their ideas. This is a fine distinction that, in my experience, is gaining popularity the last years in order to somehow remain politically correct while still aiming insults at people (cf "I don't insult you, just your religion"). In many cases, the owners of the targeted ideas will not feel the difference, and one might arue that while the difference is philosophical and sophisticated, it can sometimes appear artificial.
That a non-native speaker does not make this distinction could also be attributed to a lack of familiarity with up-to-date discourse in mayor English-speaking parts of the world.
The two together make for something that can be interpreted as a call to genocide, but even after rereading the question several times, I cannot find any reference to killing those "hated" people.
As I said, I can think of people (oh, noes! I mean "ideas") that I would love to see removed from society.
Now, in most cases, I'm quite sure that if I were to say in public that I want to remove racists from society because I hate them, I would not be charged with planning genocide.
Of course, I sound more sophisticated if I say that I deeply dislike racist ideas and I would like to see them eradicated, but even the first formulation would not give many people the idea that I am about to start killing people on a grand scale.
In short, I can see how people take offense at the wording of the question, but I can see quite easily how the question does not have to carry such genocidal tendencies at all.
That said, it would certainly not harm if Nima would have clarified the question after the questions and comments that were given.
As such, a valid reason to close-cote the question would indeed be the lack of clarity about the question and the refusal to clarify by the OP.
As for perceived genocidal motive, I don't think there is any reason to close the question.
Even if the question did enquire about genocide, the simple presence of that topic should not be a valid closing reason.
Asking how to commit genocide is clearly off-topic here, but asking how to formulate a correct sentence describing the act is not: Is the sentence "people were genocided in the war" correct?
In a similar vein, if I want help in insulting a person, that is off-topic. But if somehow I didn't manage to find a concusive explanation of the word whigger, I don't see why I couln't ask about that word and it's etymology here. Even though the correct answer would have to include one of the most taboo words in AmE.