I used to think that she's overprotective of "her team" because that's part of the often disturbing pseudofamiliar psychodynamics underlying most genre shows (one of the most interesting bits of Hannibal is how much of a manipulative bastard Jack Crawford is). But her recruiting pattern gives another, properly Watsonian reason for it. She protects her team because they are hers in a way other people wouldn't; they are personally loyal to an almost fanatical level, carefully crafted in their skills, and, to a very large degree, broken in just the right ways not to have competing interests. Hanna is possibly the exception to this, although I suspect that his combination of skills, professionalism, and emotional stability made her choose him as the interpersonal core of her team; after all, he does have a tendency to form families and care about them.
I guess what I'm saying is this: Hetty does what Bruce Wayne did, except (a) on purpose, and (b) much, much better. She must have been one hell of an asset handler-slash-interrogation specialist-slash-whoever it is that rebuilds people in useful ways. Weaponized therapist? Jason Bourner?
If only she didn't *enjoy* the process quite so much. But carefully designed emotional relationships from a position of power are tempting, aren't them? Ask Geppetto (Pygmalion's goals were of a different sort).
ETA: I know what she's doing with Nell Jones, by the way. I can recognize a Tim Drakeing when I see one.