(1) Mary Morstan is fulfilling the Sebastian Moran role, but possibly with a twist. (Many characters on BBC Sherlock are twisted.) There are simply too many parallels between Doyle!Moran and BBC!Mary for this to be a coincidence.
(2) The naming of the MP in "The Empty Hearse" as Moran is neither an accident, nor a red herring. He is a Moran, the father of Moran Doyle references as a member of the peerage connected to India.
(3) But. Moran Sr. (the MP) is actually the bad apple, the one who went wrong. He had relied on Mary's help in the past but as she's going straight for John's sake, she tried to resist him this time.
(4) Mary was intricately involved in the kidnapping of John back in TEH. She told her father where exactly John would be (that's one reason she pushed to know when exactly he was going to Sherlock). She did this partly out of fear for her secrets but also out of familial devotions.
(5) This is what "CAM" (Magnussen) threatened her with in TSOT: revelation of just why her family (her father) couldn't be there for him, because Sherlock had quite rightly just put him in jail.
(6) This is also the real thing she doesn't think John could forgive her for. Being connected to a terrorist and giving him away to terrorists to terrorize Sherlock is the equivalent of treason in his private war. John could possibly live with her being an ex-assassin if she was truly retired, particularly if there was a moral equivalent to her freelance work. But being complicit in his kidnapping by terrorists, so recently and so far into their relationship is the bridge too far.
(7) Mary may or may not have been involved somehow with pre-S3 events (the pool, St. Bart's roof). That may be a factor, but I'm not sure John would consider those things deal breakers if she'd repented, since they were before they'd met.
(8) Magnussen knew about the kidnapping but wasn't behind it. Either Moriarty is alive and saw Sherlock's return, and this was quite literally part of his attempt to burn the heart out of Sherlock, or Moran (Sr.) was trying for revenge.
So the real lieutenant of Moriarty is Moran Sr., Mary's father and the terrorist from TEH. Mary is caught up in his (their) web. And that's my theory for today. Time: 0:35, so gotta go.