Colonel Sheppard hasn't specifically asked him to call her anything else and, well, they're both still part of the Air Force, even if it doesn't exist out here. They're it. That means they're the ones that maintain order and, technically, he's the boss. So, Colonel Sheppard he shall remain until he says otherwise.

"That must be really difficult for you. Caring about Jack and having." She inhales deeply and shakes her head, a smile teasing at her lips. "I can imagine that you're drawn to a type. You pretty much told me so. Which means it makes sense that you'd still have feelings. He wasn't gone, not here, just asleep and now." She's probably just making it worse. "What'd you tell him?" And. "What'd he say?"