"Her pretty head"
This line has never really sat well with me even after watching Se7en more times than I can remember. I'ts far from a death blow, but I think just having the line "I took a souvenir" on it's own is enough to allude to Tracey being murdered. Freeman sells it well with his reaction after he opens the box and when Doe says "she begged for her life and the life of her child" we definitely know what is going on.
It's like having someone throw a bucket of water in your face and kick you in the nuts at the same time.