There has been some recent move toward creating a bankruptcy chapter better constructed to handle financial institutions; Luigi Zingales was talking about such things in October of 2008 (search for "Bebchuk" — note that his proposal makes legacy counterparties senior to bondholders, who are nominally pari passu), but there now seems to finally be an interest in this in Congress. One idea I've been batting around in my head for perhaps a year now, at least as a tool to help with these things, is the creation of a new kind of credit that the government could issue, which I call TTL cash; I know I've shared it with my brother, but I don't think I've mentioned it here.
The idea is that when a highly-connected company (AIG) gets into trouble, the government lets it go bankrupt, but any creditor who is thereby impaired is given $1 in TTL cash for every dollar the creditor lost to the bankruptcy. The TTL cash is essentially nontransferable (and thus useless) except in bankruptcy, where, in the idea's simplest form, the government redeems it for actual money. The government has not bailed out AIG, or its creditors, but it has bailed out the creditors of AIG's creditors, insofar as they are impaired by AIG's failure; the chain reaction that regulators are eager to avoid is arrested.
The slightly more general case would allow different levels of TTL cash, each of which is redeemed for the next one down; the government could decide instead to bail out the creditors of the creditors of the creditors by issuing level 2 TTL cash, redeemable in bankruptcy for level 1 TTL cash, redeemable in bankruptcy for the real thing. "TTL" stands for "time-to-live", a term used in IP, the internet protocol; each time a router forwards an IP packet to another router it decrements a TTL counter, so that if some routing error causes the packet to wander off in the wrong direction or go around in circles, it eventually gets dropped rather than continuing to be passed around.
This is, of course, still a bailout, but on a practical level the moral hazard issues are much reduced from a standard bailout; everyone is responsible for assessing the credit quality of their debtors, at least to a significant extent. One of the major practical strengths of a decentralized economy vis-à-vis a centralized one is that it recognizes the information-handling limits of agents and asks them largely to make decisions based only on local information. If you lend entities money, or even just enter into contracts with them, you have to know something about their financial condition and their other dealings that affect it; if you have to know everything about their business, including everything about their potential creditors; capping this two levels down under certain circumstances seems to me a reasonable moral hazard price to pay for the benefits of a distributed system.