One thing about financial markets is that if everybody thinks you're doing badly suddenly they don't want to lend you money and this might do you in even if your problems had been survivable. And Lehman Brothers waited until the very last moment before telling the Fed they had a problem. So the Fed insisted on throwing money at every financial institution - even the ones that were hugely profitable during the crisis.
And if your company is short on money or dying the last thing you want to cut is bonuses. If your employees smell blood they'll be thinking about jumping ship. If you stop paying salary but leave bonuses intact you'll do better at keeping people at their desks until until they've finished wrapping the company up. And if somebody screwed up in a way that contributed to the crisis they should be fired and replaced, not have their bonus cut.
THere were a lot of things that should have been done differently in the crisis. Investors in insolvent companies really needed to be wiped out to encourage them to take better care in the future. Interest On Reserves was really not needed to prevent the economy from overheating the way the Fed feared (the Fed works with numbers months out of date and they still thought the larger economy was fine and that inflation has highish when the crisis hit). The bonuses are at best a distraction but one that's easy for politicians to make sound bites out of.