Promoted to or appointed to? They’re still not political appointments, even if hand-selected by Gonzalez himself (if they were or were not, I have no idea). Anyone who’s promoted in any agency of government is technically promoted by the Secretary for that agency.
You probably don't indict a sitting US Senator with the approval of the AG, unless of course you're a special prosecutor. I'm not familiar with how PIS works, but let's stipulate it works just the way you describe.
There's a HUGE difference between the approval of pursuing an indictment and the prosecutors engaging in prosecutorial misconduct. Also, there's no allegation that Gonzales (or anyone else for that matter in the Bush Administration) knew of the misconduct before, during or after the trial. It seems to me that you (and most of the MSM) is trying to give these prosecutors the benefit of the doubt that this wasn't politically motivated because the prosecution occurred during Bush's and Gonzalez' tenure.
I believe nothing could be further from the truth. It is plausible, perhaps even likely, that these prosecutors acted unethically and even criminally precisely because if their political leanings, despite who their bosses may or may not have been.