Moriarty didn’t target Molly in TRF (2x03) because Molly was part of Eurus’s plan. She needed her alive. Mrs. Hudson and Lestrade were both sacrificeable pawns. John was targetted because Eurus knew that threatening John would guarantee Sherlock would do her bidding.
If that was already obvious to you, oh, well. I just realized it and I’m semi-proud of myself so… fight me.]