In all likelihood Crono was just intended to be an only child to a single mother. Beyond that it's just speculation. Crono's father was probably a regular man, just as his mother is just a regular woman. Thus, he was most likely taken by mortal illness or temptation. Coulda' died from a heart attack, ambushed by the monsters of the forest on the way to the castle, who knows! I really and truly doubt there’s any grand design behind Crono's father, like he's the 'entity' or he's some great grand warrior of a lost age, etcetera.