A partir do FAQ principal:
The flaming, frost, and shock weapon special abilities always have been command activated; the revision just clarified that.
Activating an energy power requires a standard action, but once you activate energy power, the power works until you use another action to deactivate it. You can activate or deactivate one of these powers on up to 50 pieces of ammunition at the same time, provided that all the ammunition is in your possession, all the ammunition is the same kind, and all the ammunition has the same power.
Any attack you make with an activated weapon deals energy damage to your foe if you hit—you don’t have to do anything special to deal energy damage with an activated weapon.
A burst weapon’s burst power is use activated and it works even when the weapon’s energy power is not activated (see the last sentence in each power’s description).
The energy from a flaming, frost, shock, flaming burst, icy burst, or shocking burst weapon never harms you while you’re wielding or carrying the activated weapon (see the power descriptions), and it will not harm your equipment. If you lose or set down an activated weapon, the energy it produces will harm other objects it touches, so it is best to deactivate it first.
Ênfase minha. Então, parece que uma vez que você o ativa, você não precisa reagir. E você pode embainhar normalmente porque não prejudica o seu equipamento. Mas, sim, você pode desativá-lo se quiser ser sorrateiro.