There was probably an effort to eliminate that episode from hitting the airwaves soon after 9/11 to give some people a chance to heal so some people took that to mean the episode was lost forever. I'm sure by the time we get to that season in the DVD releases it will be a moot point and it will be released without fanfare.
How about the X-Files movie that showed a government building being blown up. Not only did the building look like the one in Oklahoma City but the method that blew it up was so similar. If Fox didn't care about that being shown on the heals of that terror attack then a cartoon that shows no violence towards the towers should be no problem.