My thought on why John said, "It was never Aeryn," after D'Argo, standing over John and the bioloid Aeryn said, "It's not Aeryn":
I suspect he was emphasizing that this bioloid, no matter how well programmed, could never have been Aeryn. And that he was able to detect it so quickly. It was just his way of adding an "umph" (emphasis) on D'Argo's comment that it wasn't Aeryn dead on the floor. John knew that. He always knew that, from the first moment she was on Moya just minutes earlier.
So his "It was never Aeryn," to me, just means "Yeah, D'Argo, I know... I was never fooled by her, because she wasn't acting like Aeryn from the time she returned with Chiana, Noranti and Sikozu, so don't worry about me thinking I killed Aeryn, because it was never Aeryn."
I suspect that D'Argo mis-read John's emotions at the time, looking down at the dead bioloid Aeryn. D'Argo thought John was feeling like he had just killed his love, but John was telling him that wasn't the reason he was distressed. He was distressed, obviously, because of what the bioloid meant: Aeryn had been abducted and they had no way of knowing where she was.