I was more concerned Skyler would commit suicide than be killed by somebody else. Something about the way that bedroom scene was staged, it didn't seem like they would kill her there.
Breaking Bad is relentless but the deaths (Other than those in season 2) tend to be a logical consequence of the events leading up to them. At least, I would hope the writers are smart enough that if Walter Jr dies it's because Walter did something to logically cause it and not just for shock value.
That's the only way an innocent death would bother me in the finale, if it were done for shock value and not as a logical result of the story.