Those are all good suggestions.
Another way you can try is to fire a trigger after you invoke the Healing Spring that clears out the GP boxes, then regrant the godpowers the player starts with in the correct order.
For example, if the player was Zeus (Age1):
Trigger (after Healing spring is invoked): Player Kill All Godpowers effect,
Then, Trigger: Grant godpower: Bolt
This will put down the Spring, clean out the GP area, then reset it up as if you never did the healing spring at all.
If the player starts in another age (2/3/4), then just grant the appropriate GP's in order. This is also a good trick for starting a player in a later age with a custom set of GP's he wouldn't normally have.