I also think Zed saying he hopes Jonathan is ok is a bit of a platitude. I'm sure Zed DOES hope _why is fine, but it rings hollow in the context of the whole essay. Plus, who doesn't hope _why is ok. His biggest detractors aren't monsters wishing him ill.
I have to say that you confuse being an artist with being 'artsy', which is a mistake. I'm artsy, but I'm no artist. Not a single artist I know would describe themselves as simply artsy. Much of my opinion on what it is to be an artist, however, comes from the Henry Miller essay I referenced earlier. I suggest reading it. It's in a volume called "Matters of the Heart".
I believe an artist has the right to destroy his own work unless he's sold it or given it away. I'm not of the opinion that publishing work on-line is the same as giving it away, and I'm certainly not of the opinion that _why taking his stuff down is the same as breaking into a place to steal and destroy things. There's a very big difference between what _why did and your Caravaggio example. _why did nothing illegal, for instance.
In a way, _why reminds me of the French New Wave film-makers. They believed in the "film-maker as auteur" and wanted complete control over their work. From reading these forums, it sounds like most of _why's code was recovered, which is fortunate, and I'm not aware of anything missing that others collaborated on. I don't think he collaborated much with others if at all, but I don't really know. I do acknowledge that, even with works created solely by _why, there's a certain collaboration osmosis that occurs just by having it on the internet with so many users/readers/extenders/whathaveyous, but in my eyes that falls short of giving it away.
To me, _why considered his programs and their source code art equal to (more important than?) his drawings, music, poems, and stories. It was all his art. I'm extremely sad at the loss of so much of his amazing work.