I see no basis to believe that Walt would ever participate in killing Walt Jr. under any circumstances, much less Skyler doing so. It just doesn't ring true. For that matter I can't see him hurting or killing either of them.
It is hard to see, but it could happen - take for example, a big violent confrontation between Hank and Walt, Hank going to be killed, the son grabbing a gun aiming at Walt...
I'm just thinking of especially black directions the show could go, and that one does have an especially perverse evil.
They have had Walt and Jesse go from protecting to trying to kill each other a lot. So they're not ashamed to stretch these things a bit.
One minute, they're going to *extreme* lengths to protect the other - staring down the barrel of a gun of a killer - and the next day wanting to kill the other. It could be done.
I agree with you though that it'd be very hard for them to do without seeming to betray the characters and come across as artificial.
They've occassionally stooped to that - like Hank *almost* catching Walt in the trailer and falling as badly as he did for the 'wife in a car crash' ruse.
They did take some chance of betraying Skyler's character by having her ask for a murder - but they pretty much pulled that off, which seemed unlikely earlier.
So I'm not sure how they'd do it and do it well. But if they did, it's be a dark turn.