I'm not troubled by that exchange, which the NY Times included in its article today. The key to me is that they asked whether he would "stand by [his] pledge". Since President Bush's pledge apparently was only to take care of anyone who had violated the law, I don't think that this exchange can be read fairly to go beyond that. I do think, though, that he probably was inartful in accepting the question without insisting on precision.
I guess what also worries me is this prosecutor who seems pretty determined not to let this whole thing drop. Wasn't he chosen by John Ashcroft? Surely, they would have made sure the prosecutor wasn't some loose cannon that would turn on the Administration. Maybe as others have said, this is all just windowdressing to show that the investigation has been thorough and above board. So when it ends with no charges, the Libs won't be able to claim foul.