New change in 1.5: You can now remove most companions equipment and armor, and equip them with whatever you wish. Companions that are changed are Butch, Clover, Charon, Jericho, and Star Paladin Cross. Fawkes likes his new gun and he doesn't wear armor anyway, so he is left unchanged. Sergeant RL-3 and Dogmeat aren't changed for obvious reasons. I have found a bug in the removal of their default ranged weapons (not the melee weapons), and while I haven't had anyone report a bug yet, I have them still as unremovable on the companions for now.
An added bonus: You can now remove Clover's Slave Collar if you wish. Its even a wearable item if you want to wear it yourself.