Do you not think her talents would be wasted in a leadership role? Sure she has the experience, and could easily get the rank, but she might be more valuable as head scientist either way the SGC or at area 51.
She'll be the leader, so she'll be able to instil a more scientific culture and fight politically for more funding for scientific research. Basically, she'll be the spokesperson for science.
Besides the obvious of Carter, I'd say Major Paul Davis, assuming he gets a few promotions (which he is way overdue for), would be ideal.
He's been around the program for a long time, trusted by the SGC and the Pentagon and knows how to work with both politicians and with field personnel.