Since I'm the author of the filter, I gave some kind of explanation on it.wiki, that I'm gonna repeat here.
First, let's talk about numbers: the filter is up since late september, and it has about 1000 hits right now. Of course that's not much, but we can't let it go, since hits are not that rare.
I completely agree about users hitting it in good faith, though this doesn't mean much. In most of the cases, people add those tag when translating from another wiki where such tags are still used. We don't have any more obsolete tag on it.wiki, meaning they come from user intention or from outside. So, a really working solution would be to clean out those wikis as well, but that's a huge amount of job: it would be 16e+6 tags only on en.wiki.
About users not understanding the error message: that's definitely true. However it's also hard to write down an error message being both short and clear, even for those who don't know HTML at all. Since the filter is active, I tried asking feedbacks to people who hit it more than 5 times in a row, though I almost received 0 feedbacks, which made even more difficult to make it better. Moreover, we should also consider the fact that, while using CX, people don't get the right warning; instead, they're given raw code as pasted by Codas in the other topic, which would make it difficult to understand to almost everyone without good skills.
Finally, that filter was actually a warning-only one for about two months. The reason I made it block the action is that almost no-one fixed their edits without saving, which wasn't good as well.
So, no problem in making it warning-only, especially if looking forward to a built-in solution, though there isn't a true way to solve this problem right now.