It was brought up during development that That Which Was Taken can leave stranded divinity counters on permanents. You could play its ability to add a counter to your Lantern Kami, for example, and then your opponent might NaturalizeThat Which Was Taken. The Lantern Kami would still have a divinity counter on it, but without That Which Was Taken around to provide the significance of divinity counters, the Kami would not be indestructible anymore. And who wants the board cluttered up with meaningless divinity counters? Why should that counter even stick around?
However, the Betrayers development team did not want to include a similar clause on That Which Was Taken. Why? So that the card wouldn't have a bizarre, unflavorful interaction with the Myojin! It wouldn't make much sense that destroying or bouncing That Which Was Taken would suddenly, unintentionally steal away the divinity counters of godlike kami.
|The Myojin of Infinite Rage likes his divinity counter just where it is, thank you.|