It is incorrect to attribute the housing bubble to Fannie and Freddie. The loans they were allowed to purchase (remember, they don't originate any) were highly regulated and were substantially less risky. The GSE's saw significant erosion of market share in 2005-2008, due mostly to the securitization of Option ARM's, no-doc loans, etc. provided by companies like Countrywide, WAMU, Citi, and others which were being used to purchase ever more expensive homes.
If you are looking for organizational villians, look no further than the banks that went bankrupt (like Countrywide) and the survivors who had just enough strength and political influence to not fail (i.e., Citi) as well as ratings organizations who stamped anything that was an MBS with an A rating.
While the OFHEO response to changing market conditions for the GSE's was an increased allowance of low-doc loans, even so the market share owned by Fannie and Freddie was trending down until the markets broke and they became monopsony buyers of loans following the credit crunch. Then regulations were changed and we're back to the conditions of 2004 and before, where loans must be conforming, albeit with the revision of conforming loan limits for certain high cost markets. In a very real sense, Fannie and Freddie today are doing exactly what they were chartered to do. If there was no Fannie or Freddie today you couldn't get a refi, much less a new mortgage.