Caspar Weinberger had not even been tried yet when Pres. Bush pardoned him in 1992. I always thought that was a little strange, but that's not the only example.
In the case of Libby, the system has "played out" to a greater extent than it had for Weinberger or Nixon prior to their pardons. Unlike either of them, Libby has been convicted.
Well, perhaps I am wrong about that then.
Just doesn't make much sense not to let the system run its course.