The bonus issue is not as simple as it first appears.
First there's the bonuses for "ordinary" banks staff who had nothing to do with the crisis. Lets dispense with that, the cost isn't that great.
Then there's bonuses for bank staff that are contractually guaranteed - you generate the profit, you get the bonus, guaranteed. And lots of bank traders have been generating legitimate profits - even since the crash (as Idle Rich noted upthread). If you break contracts out of prejudice against bankers you set a dangerous and unethical precedent.
(The important side question is, how legitimate were the profits? Were mid-level traders paid for actual realised profit or just for "imputed profit", i.e. profit on CDSes and other derivatives contracts that weren't concluded and seemed like they weren't under water. I don't have a good grasp of that. Vim? Rich?)
Then there's the fact that senior management at banks already get their bonuses for long term performance, not short term performance. Their paid in options to buy shares in their banks whose price rises as a result of their performance - and those shares did rise, hence their historic bonuses. Of course those share prices in the toilet now, but the "cash" component of profits, based on operating profit, still applies.
Then there's the fact that much of the trouble was not caused by banks but by other FIs that exploited the fact that they were not subject to the same level of regulation as banks - especially insurance firms like AIG - who were able to expand their liquidity ratios way beyond what banks could do (but see the note below). Non bank FIs wrote vast volumes of CDSes and other instruments, betting the farm in the belief that they'd hedged their bets.
To me, the issue with bank bosses, to focus just on them, is that they deliberately tried to compromise their regulatory responsibilties and destroyed their liquidity ratios by leveraging up so much that tiny movements in underlying asset prices wiped out their entire capital, as happened with Bear Stearns, where a 0.3% drop in the value of CDSes BS held destroyed the bank. If they had simply followed the spirit and the letter of existing banking regulation then they wouldn't have got into trouble. They plainly did not. Yet they whine that regulation was too weak.
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On a separate note, I don't think that even from a libertarian point of view that the banks should have been allowed to fail - not wholesale, not systemically. It might be intellectually satsifying. But the real human collateral damage would have been far worse.