A former Bush aide even tells the magazine that deep down, the president himself probably suspected Libby went to jail to cover-up for Cheney.
From the Time article:
http://www.time.com/time/politics/article/0,8599,1912297-1,00.html And there was a darker possibility. As a former Bush senior aide explains, “I’m sure the President and (chief of staff) Josh (Bolten) and Fred had a concern that somewhere, deep in there, there was a cover-up.” It had been an article of faith among Cheney’s critics that the Vice President wanted a pardon for Libby because Libby had taken the fall for him in the Fitzgerald probe. In his grand-jury testimony reviewed by TIME, Libby denied three times that Cheney had directed him to leak Plame’s CIA identity in mid-2003. Though his recollection of other events in the same time frame was lucid and detailed, on at least 20 occasions, Libby could not recall details of his talks with Cheney about Plame’s place of employment or questions the Vice President raised privately about Wilson’s credibility. Some Bush officials wondered whether Libby was covering up for Cheney’s involvement in the leak of Plame’s identity.
That meant taking up the pardon question again was, as a West Wing veteran put it later, like passing a kidney stone — for the second time. Bolten declined to take a stand, according to several associates. Instead, he lateraled the issue to Fielding, claiming that a legal, not a political, call was required. If the counsel’s office decided a pardon wasn’t merited, says an official involved in the discussions, everyone else would have cover with Cheney. “They could say, Our hands are tied — our lawyers said the guy was guilty.”
The magazine also reports that “In private, (former President Bush) was bothered by Libby’s lack of repentance.”
more:
http://rawstory.com/08/news/2009/07/23/report-some-bush-officials/