Well, that's the big question - whether Sherlock "dying" is proof that she did mean to kill him, or whether it was added for dramatic effect.   I think it's probably the latter, for various reasons, but mainly because of Sherlock's deduction - if the fact of him almost dying meant that Mary meant to kill, then he wouldn't need to deduce any further.  He would know that.   So unless he's fooling us with his deduction, he believes that she didn't mean to kill him.

There was a little bit in the commentary where Steven Moffat said he wished he'd added something about Mary's aim not being perfect when she shoots the coin, which implies to me that he wished he made it clearer that she didn't mean to do so much damage.  Of course, it could mean that she meant to do more damage ... but then I'm back to Sherlock's deduction again!   

I think that story-wise, there's a scene where it looks as if Mary tries to kill Sherlock for certain (she says she's going to, he thinks she's doing it, etc.), and then it's "revealed" that that wasn't actually her intention.  It doesn't work if she was trying to kill him all along.  

We will find out for sure in a few months time, though - there could be yet another twist!