General Mattis deserves to be able to pick and choose the persons he respects and trusts to serve under him at DOD. Don't be shocked if his tenure at DOD is a short one if the President won't extend that ability to him.
Even Generals make mistakes. Farthest I ever got in my Army career was respectfully telling my Group Commander his assessment that "there are problems regarding accountability in the S-4 section" couldn't have been more incorrect.
Long story short: my counterpart, the Group S-4 (a major) was unable to conduct the inspection, so he sent his assistant, a butterbar. I had to be in the mission briefing with all the brass, so her questions had to be answered by my Spec 4. It wasn't his fault, and I told him so...he never should have been put in that position.
I stood up and told the Grp Cdr that I knew where "every dollar in our budget went", and that he could confirm that statement with his S-4. The minute they left, I called the Group S-4, advising him that LT of his was no longer welcome at my HQ.
It was sorted out by the next afternoon. The "old man" (Battalion Cdr) called me into his office to inform me (with a wry grin), that the Grp Cdr apologized for the "misunderstanding. No harm, no foul. I continued to work for him when we were transferred back to the States (Fort Bliss). He was promoted to O-6, and he installed me as his Operations Officer, an O-5 slot (good for the ego, didn't increase my pay any, had been a Captain about a year...lol), in the agency he commanded at Fort Bliss.
I'm sure Mattis got along with her fine when they worked together at the Pentagon. However, if I read it correctly, Flournoy turned down his first offer. Given her history, she should have been shown the door on 1/20/2017.
