By definition disarmed means "deprive of weapon, reduce armed forces. 2. Make less hostile; win over." Satan and the archangels are not going to physically take away the "Thunderer's only dreaded bolt" they are taking away the universal belief that God is the only one with this kind of power, God is no longer unique in the possession of this weapon. Satan believes that he now is that much more of an equal to God because he thinks he has come that much closer to overthrowing God and taking control of heaven.
The reference to the "Thunderer and his only dreaded bolt" is a forbearance to further along in book six when Christ strikes down Satan and his army with a hand full of ten thousand thunder bolts. Zeus was the King of the Gods and the King of Thunder. Here Milton seems to combine both Christ and Zeus together as one God.