I don’t think cortana had control over the domain. Humans were the intended reclaimers so she needed chief to give her access. She used the guardians call back to home function to rig a way to bring him to her, and then she had him activate the portal structure by placing shields and directing him to open them so he could “get to her”. Chief opened the door to the domain and let her through. She used chief to get the mantel of responsibility. I imagine that she wanted to keep him so he could access more stuff for her if she ran into that need later on. She manipulated chief the entire game and lied. The mantel was never meant to belong to the “created”. She knows that the mantel is for humans, but in her rampant state she decided that she was better suited to use the mantel to enact control over the galaxy. Even if her end goal is good, she is willing to slaughter as many as necessary to reach that goal. She no longer cares about chief or humanity, she just wants power and control now.