The beam overload skill is still glitched and puts weapons offline for the duration of your mission but it seems to affect the actual weapon its self not your ship, So the best thing you can do is carry a backup weapon to swap out with the offline weapon. Its not a perfect fix but it can make it so your not down a beam weapon or two during a mission/pvp.
There is some confusion for what this post was about, the "fix" is for the glitch that occurs from using the BO skill beam overload. The glitch being that one of you beam arrays (the one that was oveloaded) goes offline permenently and wont function again untill you start a new instance ( or die?)
By switching the weapon out for a new one you can again use all your beam arrays.
(however until you start a new instance you can't re-equip that beam array and have it work)