It will be interesting to read how this continues; I suspect Joel knew quite well that his negative comments about Ruby would garner some real attention and require some follow up.
I'm also not sure I agree with all of Atwood's points.. I think one could make an argument on behalf of Joel that goes something like this: Rather than choose to write the product in a fixed language that would hold us captive to that platform, we built a homebrew language well suited to the product so that we could change the target output when that becomes more advantageous. I agree with Jeff that this is usually a very bad decision, but there are long-term projects where it might make sense. It's also not clear to me how windows-centric Joel's product is; if the answer is "very" then it seems to be that the argument against using Ruby makes more sense.