It may be that Rowling had never thought that far afield when planning her novels. It may be that she did think of somewhere that he went and it will be included in the oft mentioned encyclopedia that she may publish at some point in the future.
Since Slytherin's descendants now went by the name of Gaunt, I assumed that they somehow married into the family of John of Gaunt, son of Edward III and Duke of Lancaster, but there is another Gaunt, who owned the lands where I thought Little Hangleton was placed on. This Gaunt was Gilbert of Gaunt, a knight from Flanders who came over with William the Conqueror. This Gaunt was also possibly godfather to Hereward and nephew to William's queen, Matilda. This provides Hereward with a powerful friend to reconcile the king to him and any that broke through the siege at Ely with him.
Once the surviving resistance leaders like Hereward or Edric the Wild were reconciled to the king and other potential leaders like Earl Morcar or Earl Edwin were dead, was there any point in carrying on the resistance? And even if you could defeat William, who would you replace him with? Edgar the Aetheling should have been the heir to the throne but he was not able to attract the following that Hereward was and possibly lacked the talent in tactical matters that Hereward seemed to have. Even with Earl Morcar, one of the most important of the remaining Anglo Saxon nobility and an heir of the Mercian royal family, at Ely, Hereward was the resistance leader. So, would Slytherin, by now an old wizard, want to carry on a bush war that had no hope or would he opt for peace and settle on a bit of land?
The other piece of the Gaunt family history, the Peverils also settled in the same area of Little Hucklow ( my candidate for Little Hangleton) where William Peveril, a Norman knight and possibly William I's bastard had a castle.
Another question would be - did Slytherin marry late in life after the pardon by the king or did he retire to a farm with a family that he already had? This is my guess then. He already had a family, took a pardon and retired to Little Hucklow and his only daughter or granddaughter caught a Peveril or (most likely, since the Gaunts were Flemish and not of the hated Norman invaders) a Gaunt eye and so the family name was lost, although the genes and propensity for talking with snakes was passed on.