The problem here, is that we don't know what steps led up to the suspension and what was actually said to the child/parents.
Unfortunately, though, as stupid as it may seem, this is a rule in many schools. It is a rule that is grounded in some thought somewhere. It may not be one with which people agree, and there are many rules with which people don't agree, but if one chooses to disobey a rule, they choose to accept the consequences.
I just re-read the article. The child was counseled twice about his behavior, once by the assistant principal, and once by a counselor in an "extended conversation." The child's parents were also spoken to by the assistant principal and warned that further incidents of this nature could result in suspension. I'm not sure how many more "warnings" the school should give.
Maybe the child didn't see the gesture as threatening, but the girl whom he did it to did. In light of Sandy Hook, this is very possible. Also, it's the parents and their attorney's side of the story that he said "pow" and was playing, but since neither was there to witness the incident, other than the child's say-so we don't know if that's what truly happened, or if there is more to the story.
I guess my point is that it is a rule. Had it been my child and he had been spoken to twice, as well as I had been informed that another such incident would result in suspension I would make sure that my child knew that he wasn't allowed to do this at school, whether I agreed with it, or not. It's not going to stifle a child if he is told he can't play guns only while at school. There are a ton of things that kids are allowed to do at home that aren't appropriate at school.