Dude, he kisses her goodbye and calls her his girl. I think they’re cool with each other. They’ve totally gotten over that shooting thing. Other people wouldn’t get over finding out their wife had this whole other life in black ops and most dudes would not get over getting shot by their best friend’s wife. So there’s that. So I get tired of the mary hate. mary is awesome and they both love her in their own unique way.
I am 100% sure Sherlock and Mary were joking with each other about that time she shot him the day after she revealed the truth. Like, Sherlock would use it an excuse for Mary to do stuff for him.
"Mary, can you get me biscuits?"
"I just sat down Sherlock. And I’m pregnant."
"Remember when you shot me?"
"You don’t get to use that excuse again for a whole week!"