What a fine example of "game design"
Retail, old core, other private servers (not to mention every other game that comes to mind) do not have such a faulty spam filter - faulty as in prone to generating false positives. Maybe the problem is the implementation of this very filter, not every other product out there.
If the spam is bad enough, as you say, it's because this filter works only in a super short window; if you wait 1 second or so between messages you can still spam... false positives AND false negatives, yay.
There are ways to improve it without hindering its effectiveness
1) Use progressive penalties, so that heavy spammers get the full penalty effect while mistakes only mute you for a few seconds.
2) Make the filter mute you only where you can trigger it. The filter only procs in SAY, YELL and CHANNELS. But when it procs, it blocks ALL communication (party, raid, whisp). This doesn't make any sense imho.