FDIC Chairwoman Sheila C. Bair, together with JPMorgan Chase (JPM) CEO Jamie Dimon shared the spotlight for saving Washington Mutual (WM) depositors without costing the government a dime. The story is old by now; JPM got the good and the bad of the bank without the holding company’s ugly debt. (Think Clint Eastwood.)

After the glory fades, the reality will come out that the FDIC cannot be trusted. JPM and others were conducting real negotiations with the FDIC at the same time they were conducting fake negotiations with WaMu’s management. During the consummation conference call, Jamie Dimon disclosed that JPM had unprecedented access to WaMu’s mortgage detail. JPM received computer tapes with the most granular mortgage detail (FICO scores, LTVs, and MSAs) to compare with their own data and develop loss projections. JPM had the time to do a true bottom up analysis.

I do not know if it is common FDIC practice to negotiate the sale of a to be closed bank without informing management. But in this case, it sabotaged WaMu’s effort to sell its valuable branch system. I also do not know when the FDIC undercut WaMu’s management. Was it before or after the fall of Lehman? WaMu started to face a bank run on September 15 – the day Lehman filed for Chapter 11.

The FDIC alone could be proud of its accomplishment, but in the overall context they further eroded investor confidence. Now the moral hazard has spread beyond equity holders to bond holders. While WaMu had been slowly losing deposits, the fall of Lehman (LEH) and subsequent nonstop media coverage accelerated withdraws. The $16.7B (9%) deposit loss since September 15 alarmed regulators.

We are on the cusp “investing” $700B in government money to liquefy toxic bank assets and rebuild investor confidence. We got here through a series of miscalculated idealistic policies based on moral hazard. At this juncture moral hazard has proved extremely expensive with little investor confidence to show for it. Surely backstopping a Barclays (BCS) purchase of all of Lehman and a JPM purchase of all of WaMu would have bought a great deal of investor confidence at a cost far less than $700B.

Where does this leave Wachovia (WB)? The stock market and the media would have us believe that the vultures (the mode of JPM) will wait for the FDIC to serve them the carcass. There are many reasons why it is not in the best interest of the government to let that happen. Beyond the shock to investor confidence, the United States should not be limited to a handful of mega banks. JPM, Bank of America (BAC) and Citigroup (C) need competition.

The Paulson/Bernanke team has not been very pragmatic in creating value in the form of investor confidence for their bailout money. Punishing or killing shareholders and now bond holders have proved very expensive to the government. With each new implementation of moral hazard, the government has to lay out more money to lift investor confidence. The latest trade off – forgoing possibly $60B in Lehman and WaMu backstops created the need for Paulson’s $700B market maker fund.

If the government lets another large financial or insurance institution fail, or severely punishes their shareholders, Paulson $700B slush fund would be the same as you know what in the wind. Proactively, the most cost effective thing the government can do to prevent bank runs is to raise the FDIC insurance limit from $100K to at least $1M for individuals and $5M for businesses.

Disclosure: Author is long BAC, C, JPM and WB.