Eric, your speculative reconstruction of the Hale family is worth testing, as long as it is clearly identified as speculation. So let's test it...
First of all, you appear to be assuming that William's son Thomas (alive and adult in 1625, no further record) is the same as Thomas Hale-459. The available evidence (Thomas Hale-459 was older than William's heir Rowland) appears to conclusively disprove such an assumption.
It appears that, if we set aside the speculation that William's son Thomas was the same as Thomas Hale-459, there is no evidence that William's son Thomas was the son of an earlier wife, or that William had an earlier wife. (If you have any information about an earlier wife, I would be pleased to be informed.)
The biggest problem with your hypothesis is the speculation that George Bond made a marriage condition that the children of Rose be sole heirs. Such a condition would be impossible, because of the law of primogeniture. William inherited Kings Walden as his father's eldest son, and by law was required to pass it on to his eldest son, or (if that son died before him) the eldest son of his eldest son. He couldn't disinherit his eldest son simply because of the demand of a lordly father-in-law. This, by itself, seems to prove that Thomas Hale-459 could not be the son of William.
And furthermore, as you already demonstrated, in 1625 William's son Thomas was lord of the manor of King's Walden together with William, which means that Thomas was William's heir, which means that there was no deal to pass over Thomas in favor of a son by a second wife, which brings us back to our two earlier possibilities: (1) William's son Thomas died (without having any sons) before William died, or (2) William disinherited his son Thomas.