Point 1: The fine proposed against CBS is $272,000. That just a little over what a single 30 second spot aired during the show would have cost. CBS won't miss it. The only danger here is setting a precedent and I'm sure they'd like to avoid that. The fine itself is peanuts.
Point 2: Here's the real doozy. Take a look at the descriptions of everything that went into downloading an actual EAS message (from Youtube *sigh*), modifying the EAS tones, testing them to make sure EAS decoders weren't tripped and so on. The episode takes place around 1989. EAS wasn't implemented until 1997! Everything they did with the EAS tones was an anachronism and completely unnecessary. The system in place at the time was EBS (Emergency Broadcast System) which only used the 853/960Hz dual tone attention signal. The editor could have simply substituted a 1000Hz reference tone and it would (IMO) been just as effective since the offending sounds they did use were buried under two levels of dialog and a music bed. (You can watch the scene for yourself and judge: www.youtube.com/watch?v=z9gIRB3jLvc )
This got screwed up on both sides pretty much as badly as it could have been.