And here I was starting to think that MJ would be the one who get's shot. And isn't interesting how everyone seems perfectly okay with Aunt May getting killed. So much for respect for the elderly
There is the possibility that those images from the Annual are a flashback to the Amazing Spider-Man 1987 annual and that the other page with Peter, Gwen, MJ, and Harry is a kind of "Untold Story," but considering the recent FNSM #17, it's a pretty good guess that Aunt May is the one who gets hit by the snipers bullet (I'm reluctant to say dead because it could be a situation where Aunt May is hospitialized and in a coma, just to drag out the drama). Plus, it actually makes sense on with regards to dramatic irony--Aunt May more than anyone was the one who convince her nephew to publicly reveal his identity as Spider-Man even though Peter knew it could potentially put her life in danger, and then sure enough, the very person who persuaded him is the one who winds up on death's door.
I will agree however that the notion that MJ would be perfectly okay with Peter wearing the black costume when it's been established that it scares her and reminds her too much of Venom would be a continuity gaff. Then again, it's possible that Peter dons it because his red-and-blues are ruined from the battle taking place in Civil War #7, that he has no other spares but the black one, and that perhaps he sends MJ further into hiding in a separate place from him in order to protect her, restoring to secret mettings and what not, so perhaps she doesn't have much to say about the decision of him wearing it.