When a Sanctuary's Decay counter reaches zero, its ability is immediately activated for the rest of the game.

This is supported by the following:

• On page 20, it states:
  "As for a Sanctuary’s Decay counter, it automatically decreases one space during each End of the Turn phase (8.4) of its controller. Once it reaches zero, the Sanctuary’s ability is immediately activated."

• The End of Turn phase order on page 26 is:

  • All partial damage on Units is reset.
  • All your Units become active.
  • All your Sanctuaries decrease their Decay counter by 1.
  • Resolve all “At the end of your turn” abilities and effects in any order.
  • Discard cards as needed.
  • Draw up to hand size.

The Decay counter decreases before resolving "At the end of your turn" abilities. Therefore, if the Decay counter reaches zero at this step, the Sanctuary's ability is activated immediately at that point, before any "At the end of your turn" abilities or effects are resolved.

Summary:
A Sanctuary's ability activates immediately when its Decay counter reaches zero, during the Decay decrease step of the End of Turn phase, before any other End of Turn effects are resolved.

Source:
Page 20, Page 26

Source: Core Rulebook (pp. 11, 20, 22, 23, 26)