Hmmm, Deep Gates. I know in the game where I steamrolled the world the two Deep Gates next to the stratospheric citadel made destroying it particularly painful.
In a way I kinda liked the old Deep gates. Honestly, I'd like them to go back to the way they were, BUT with some interface improvements and warnings. Since you're working on the auto-purification display, why not add another element to it that will highlight any Deep gates that would also be activated? Then, when the player goes to embark into the tile that will result in a Deep Gate being activated bring up a prompt that educates new players and warns them on the impending activation with a choice to cancel, similar to the dialog that pops up when you try to enter a purified tile with no perk tokens.
This way, you can have powerful Deep Gates without the pitfall of players accidently opening them. Players will have to consciously weigh the pros and cons of purifying that tile once they are properly informed.