Well, I do have to say that her apparent take on the characters, and on John in particular, is not my take. For example: "John shoots people. He shot the psycho cabbie in episode one, and that was fine. He beat up a crack addict, and that was fine. So, Mary fits in really well with those two. They’re all psychopaths." I do hope she's joking about the psychopath part. I mean, John shoots a serial killer who's trying to poison Sherlock, and he disarms a guy who's trying to stab him -- and that makes him a psychopath?!
I wish she had elaborated on the "redeemed" part. It seems to me that her shooting Sherlock is either justifiable on the spot (and I think a good case can be made for that) or it's not justifiable at all. If she's talking about Sherlock's "surgical precision" claptrap, I don't see that as redeeming her. I think that was just Sherlock's way of giving John his permission to work things out with Mary.
I've been questioning my sanity ever since I saw this episode. Maybe I'm just sensitive, but if I were in John's place, I'd would be mortified, terrified, and angry beyond all rational thought. The woman I love, who is carrying our child, nonetheless, is not who she had said she was. Worse yet, I'll never know the truth.
I think of it like this, John is not only Sherlock's friend, but he is also a survivor of war. He is no stranger to excitement and chaos. I always viewed Mary as the perfect person for John, because she brought a sense of comfort and normalcy into his life. Their life together seemed like the perfect escape from the trials of Baker Street and Afghanistan.
I guess that's the difference between myself and Mr. Watson.