You can not cast with the wizards tower during either quick cast phase. It can only be used during the creature action phase before or after you activate a creature. Now you can also use the quick cast marker during the creature action phase before or after activating a creature, so during that time you could use the tower after a quick cast.
As others have pointed out, thunderbolt was an illegal bind, but there are other attack spells with decent stun chances, so the question of how to combat it remains relevant. I would recommend storm hide armor to reduce the damage and stun chance, possibly combined with elemental cloak. -3 to the stun chance is pretty big. I like this better than running away as the warlock probably wants to be aggressive. A block spell to stop it for sure though is a good idea. Destroying the tower is risky though because the wizard might have another one. Separating the tower from both mages with a wall could work, but only if you are both on the same side of the wall. If you leave the wizard with the tower he will be able to simply build up better than you and crush you at his leisure.