Being in Facility has made Sakura incredibly aware of physical contact, and very little of it has been positive. After being murdered, Sakura cannot stand being pinned up against the wall or on the floor by anyone, and her neck and ears are right out for casual contact.
Madara intensified this; there is no part of Sakura that's comfortable with being dominated in those fashions, with or without sexual connotations. Pinning her down is a guaranteed way to get her to be extremely, extremely pissed off at you.
Part of that is due to fear.
She doesn't feel as comfortable with Naruto being from an earlier time than she is; she wants to protect him, but it doesn't feel right to protect him from what she cannot change.
She's pushing herself hard personally to work through her nightmares related to this place, and to a mixture of this place and memories and fears from home.
She's not coping with her nightmares very well. Meditation techniques are all that have been sending her to bed lately.