So I cannot wait until all his library is milled then Tormod's Crypt him? Because I was hoping that Gaea's Blessing would not take effect until after all the library is milled. Then I was hoping to just stack my Tormod's Crypt and remove all the Blessings at once.
Yes you can, that is if you mill all the library in one shot (not with Brain Freeze).
Here is what would happen with let's say Painter and Grindstone.
You mill their library
Blessing #1 goes on the stack
Blessing #2 goes on the stack
Both players get priority and can use spells or abilities (Tormod's Crypt)
Blessing #1 resolves, you shuffle all
Both players get priority again
Blessing #2 resolves, you shuffle all.