Here's the original article cited in the article HM posted. Unfortunately, neither article has the Justice Dept. e-mail in it's entirety reproduced. It would be nice to see the date of the e-mail, and if it came after Bush's taking responsibility.
I have no problem with an independent inquiry looking into all the possible causes that led to this disaster, including this one, but this looks like a coordinated smear campaign against environmental groups in order to shift blame away from the Bush admin.