I think you're heavily exaggerating the way in which SJIS/JIS conversion is broken.
First off, this is only one bug report. Yes, there have been others, but there are probably as many Unicode related bugs reported than SJIS/JIS related ones, if not more. In fact, NineTails commonly reports SJIS/JIS bugs (he's probably the most common bug reporter for that feature), but if you look at his history he's made just as many reports about UTF-8. So, to make the claim that SJIS/JIS is fundamentally broken just isn't right.
Secondly, NineTails is reporting a rather uncommon use case here. While that's no excuse for the bug-- I would bet that most users who speak Japanese on IRC don't also speak Russian (or other Cyrillic languages) in another channel on the same network-- maybe English, but there would be no problem there.
This can and should be fixed, no question about it... but I think you're magnifying the way it affects the userbase; it is likely not nearly as bad as you make it sound. SJIS/JIS is not nearly as broken as you make it sound, or the bug report here would have been "SJIS/JIS BROKEN ALL THE TIME", not "SJIS/JIS not working when I speak one language on one channel and another language in another while eating cheesecake on tuesday" (exaggerated to illustrate my point).
Finally, UTF-8 is not the answer. As I mentioned before, there have been just as many posts about bugs in Unicode as there have been about SJIS/JIS. This entire conversation could have been about some Unicode issue just the same. Would you have suggested trashing UTF-8 in that scenario? No. Because you like UTF-8.. I assume you don't mind ridding the world of SJIS/JIS because you don't like or use SJIS/JIS, and it would not affect you.. well that's not fair to those whom it would affect.
Throwing out a buggy implementation is not the answer. If Khaled respects his users, he'll fix it because they rely on it. That's the real answer.
As an aside let me add that this post actually belongs more in the Feature Suggestions forum than the Bug Reports forum. Khaled had already mentioned that SJIS/JIS is intentionally applied server-wide because of the way the conversion works.. so it's not as if this behaviour is broken, but rather, not even implemented to behave the way NineTails expects. Now, you were right when you said it's probably a difficult task to undertake, and I would guess that Khaled tried and then scaled his solution back waiting for someone to specifically ask for such support (perhaps hoping no one would). However, difficult is not impossible, and there are ways to implement this.. we will see what Khaled chooses to do.