Actually, it was good for JONATHAN stealing the guns. And, yeah, it doesn't make sense that JHI wouldn't check his van first before leaving, but whatever, he's gone for now. I'm guessing he'll figure it out soon enough, and that will be the reason he returns.
As for what Jon said to his grandfather ... weeeeeellll, I'm not so sure Jon is telling Sam the whole truth. I'm sure it's the truth he wants to believe, that his father and brother would never hurt himself and Lois. But that's not true as Jordan already hurt his brother, and Jon did watch Superman kill Lois on another world. I'm gue