There is a real risk is that the gov't will start to throw its weight around once it has a large stake in a bank. It may start to pressure the company to make loans it wouldn't normally make or to support legislation that it wouldn't normally support.RF
Case and point, Freddie Mac and Fannie Mae circa mid to late 90s. These government sponsored enterprises (GSEs), responsible for buying mortgages from banks, were leaned on heavily by the Clinton administration (HUD specifically) to buy up increasingly risky loans from lenders in a effort to get more Americans into homes as part of the 1994 National Homeownership Strategy. If the federal government did not have a stake in this institutions, I have a hard time believing that they would have been willing to buy up any subprime loans at all.
I think another problem is that the federal government is not equiped to handle oversight of large corporate entities, let alone the day to day administration.