A decentralized currency should not rely so heavily on a central exchange.
The majority of Bitcoin trade occurs at Mt.Gox, so you could say the market is pretty centralized.
Actually, Bitfloor had to cease all trading operations indefinitely. That aside, there are plenty of other reputable exchanges that need to gain more market share. It's ridiculous that a DDoS attack could be used for price manipulation purposes. That shouldn't be too much of a problem in a diversified market.
There are also a number of pastebin / IRC logs shedding more light into the dispute. Doesn't make a lot of sense, but it makes slightly more sense than the other theories I've seen proposed.
I hate to sound all conspiracy theory'ish, but I can't help but wonder if a State actor is involved in this. While Bitcoin might not be (by itself) the techno-libertarian / cypherpunk / crypto-anarchist Holy Grail that some people make it out to be, I expect at least some governments to fear it on some level... if for no other reason because it's something new and they don't understand it.
Or maybe it's being done by backers of a competing crypto-currency? Hmmm...