From that Grantland article, a good theory on why Walt has probably already murdered Skyler before the Denny's scene (I'm hoping this happens for all you "Walt cares about his family more than anything" people):
In Breaking Bad, Walt has a habit of taking on some little traits of the people he has killed.
When Walt killed Crazy 8, he started cutting off the crusts of his sandwiches — just as Crazy 8 had done.
Gus drives a Volvo. After Walt kills Gus, at the beginning of Season 5 (at the Denny's), Walt is driving a Volvo (w/ NH plates).
When Mike and Walt meet at a bar in an earlier season, Walt orders his drink neat while Mike has his on the rocks. After Mike is killed, and Hank offers Walt a drink in his office — he asks for it on the rocks.
At that same scene at Denny's, Walt arranges his bacon into his new age. Someone else used to do that. On top of that, he's using Skyler's maiden name on his fake ID.
Based on his history of picking up traits from his victims — I believe Walt is going to murder Skyler before the series is over, and it probably had already happened before he showed up at the Denny's in the Season 5 cold open.
Jesse too:
BuzzFeed also
adds two more elements from last week's episode: Walt folds the towel in front of the toilet when he gets sick, just like Gus did when he was vomiting out poison; flash-forward Walt is wearing Jesse's jacket, foreshadowing (and also reverse-shadowing, because that's what happens when you shred the narrative continuum) that he must have killed Jesse as well.