Suppose, there is a question, which follows the guidelines for asking a question on this site. But, OP aren't being cooperative and nice in the comment section. Someone flags those comments, all the comments are therefore, ultimately cleaned out by mods.

But, some users, voted to close the question as off-topic (the question is actually on-topic) because OP sounded bad to them.

Is it good/accepted to do so?

Something similar happened with this question. This is a nice question IMHO. Yet, it was voted to close. Other respectable users also followed and voted to close the question.

The question I linked was closed under the head : "This question is missing context or other details". (Reopened now, after this meta post from me)

I think this isn't OK, because when the comments are deleted, and the question remains closed, future-visitors will never come to know that why was this question closed in the first place.

So what is the correct way to deal with such users, who ask good, but apparently don't behave good. Is closing appropriate? If not, then what should be done?\

I am posting this, after this one, where I learned that OP wasn't behaving nicely, which probably was the major reason for closure. In the linked meta-post, I assumed, that the users who voted for closure, did so because of not paying proper attention. I apologise for that. But after knowing the reason for closure, I ain't satisfied either.