So there is a button to make Armor and Utility Items available, that is take away from those not on the mission, but there does not seem to be an easy way to make guns available. With modded weapons, this is a big pain to switch the guns out from injured people. Am I missing a better way to do this?
There is no way to do this in the base-game, you'll have to go through and remove them one-by-one.
However, fortunately there is a mod that adds a button to remove them all at once: Strip Primary Weapons