Well, given the nature of David's rather confused behavior about Shaw... I mean when he knew she was preggers with black goo baby he did want to throw her into stasis. Granted he made a poor taste joke later on, but...
No, he seemed to care about her on some level, or at least have some affection. So for all we know he had her unconscious/semi-conscious/sedated in a Hannibal Lector type of situation. That's just what I'd prefer out of my psychotic villainous android. The kind of thing he did at the end of Covenant where he hushes uh... What's her name again? The one. Ya know. Survivor.