"Almost as bad as the lying is accusing your DS1 of lying here. The only way your DH could cover his own dishonesty was to make out DS1 is the liar."
I would say that the accusing your son of lying to cover his own dishonesty is worse... far worse, than the lie itself. Your son did the right thing. He told the truth to you about his father having left him and his younger sibling at home alone.
Your husband knew that when he said "oh, don't be daft! Of course I didn't leave them on their own... [son] is lying again!", he would be ensuring that your son was told off, by you, at the very least, for lying.
But he wasn't lying, was he?
"It will destroy all trust the little one has in daddy, because he knows when push comes to shove, daddy will chicken out at all cost."
Yep. This with spades on. My ex (and, again, please... please notice the "ex"!) accused our then 2 year old DS of lying to me. Consequently, now he sees exceedingly little of DS, which is DS' choice. Because that lie to get our son into trouble... didn't stop there. The lies escalated. Like you, I tell the truth at all costs. Because that is how I was raised. It's how I have raised our son. Who still tells the truth - no matter how damaging that truth may be. My ex? Well, he still lies (mutual friends) and, according to ex-MIL, is now having problems (of his own making) with the fact that his younger child is telling horrendous lies at school. I count my lucky stars I'm no longer with him and DS knows that telling the truth is far, far preferable to lying.
And if I were you, OP, I might be asking myself what else he's lying to you about, in front of your son(s) - or not!