Steven Moffat (writer and producer for Sherlock) sheds some interesting light on Episode 1. I've excerpted some of the most important parts of the interview below.
On Mary's Death:
Yes, we’re not playing games. She's [Mary's] dead.
On the topic of the Sherlock-Watson relationship:
We take that rift head-on in the remainder of the [season]. We don’t ignore it. We don’t have John come back and say, “Well I’ve thought about it and it’s all fine.” If anything, the rift gets worse.
Sherlock's culpability in Mary's death:
We spent a long time trying to work out what his culpability was. Obviously, it wasn’t his fault... But having Sherlock unable to stop himself from showing off and that’s what riles her up to take the shot, I think it adds another layer.