Yes, you can remove then when they are banished, as all boon. The main difference is that you cannot refuse to make a check to acquire a Blessing of the gods when you encounter one, so you have to take them. But a Blessing of the gods is banished for other reason (such a from closing a location), it can be remove from the box.
Concerning the main topic here, i understand the arguments for changing the banish rule compare to the board version of the game, but i still find this quite disappointed. I was looking for removing definitly all basics from the vault, which you have required a lot of game played for each party. In this version, i will play less.
