It's just a little bit of a cheat to have Todd to step up to the plate unasked and shoot the kid. Will Walter think Todd's a tradeup on Jesse?
Not making it necessary for Walter to give the order is at least defensible. I don't understand how Skylar could possibly think she can keep Junior/Flynn away from Walt when she won't even bother to give the kid a reason. She has to know that all she's doing is leaving Walt the opportunity to paint her as the villain. If she really wants to keep Junior away she has to say something.
The recap included Walt saying the melamine must flow. This is to my ears a blatant allusion to Dune, and Baron Harkonnen. (Ian Macniece or Kenneth MacMillan, take your pick.) Who knew Walt was an SF fan?