I think the hearts the EQ extracted were the person’s soul. It took on the tangible qualities of a human heart in size and appearance, but it was really a metaphore for a human soul.
When Emma was close to Graham she said something to the effect of “…there, I can hear your beating heart. It’s there, I can feel it” just before they kissed. It’s non-sensical to remove an actual beating heart and have the person still walking and talking.
I think the heart is Kathryn’s but I can’t shake the feeling the writers are dangling another red herring for us to grab. Emma did get hair samples and DNA evidence from the car accident, right? I don’t remember he saying so, but she probably sent that evidence along with the heart to a lab for a match.