Was Carmela and AJ killed?

Because of the dramatic subject matter and the contemporary setting, we – the audience of The Sopranos – have a tendency, if not a desire, to view the show as a window into an alternate reality. For example, when Carmela says “You may not realize it, but you are making contacts,” we like to think she is doing so because that happens to be the thought going through her character’s head at the given moment. When the scene cuts from a discussion between Meadow’s and Patrick’s families to a cat at the Bada Bing, we like to think we are just witnessing the next relevant happening in a chronology. When AJ develops a relationship with a girl named Rhiannon, we like to think that just happens to be the name her parents chose to give her.

However, The Sopranos is first and foremost a work of fiction. And as such, it is likely subject to all the plot development devices commonly employed by authors of fiction including: dramatic irony, symbolism, and meaningful scene sequencing. Using an understanding of these techniques to glean clues from the final two episodes, we can clearly conclude the following:

Tony was indeed “whacked”
Carmela and AJ also were killed
Meadow lived
Patsy Parisi betrayed Tony
AJ inadvertently facilitated the murders
Rhiannon was an unwitting accomplice for the murders
Here I will take the most important scenes from the final two episodes – mostly the last episode – and break them down piece by piece. The analysis is chronological. However, any scene and/or line of dialogue deemed as nonessential to the analysis has been omitted in the interest of brevity.
Episode 85: The Blue Comet
Silvio: Burt let me know the other night he’s been playing both sides of the fence with New York.

Tony: Burt?

Silvio: Measures were taken.

[Tony looks at Silvio’s bandaged hand.]

Silvio: Burt wasn’t speaking for just himself. Guys are getting squeezed hard to sway them towards new management.

Tony: They thought you’d be a part of it?

Silvio: And he got an answer.