Sonny's witnessing the murder of Fanucci is to me very relevant. It would explain a few things, but most importantly the "BADA-BING!" phrase Sonny keeps using - think about when he is lecturing Michael on what it is really like to blow someone's brains out. Fanucci's murder clearly had a lasting affect on Sonny. When Vito finds out, I think a lot of things in his head go 'click' and he understands a bit more of Sonny's nature. This is why he backs down to him. It saddens him.