Let's use your scenario (which I think I described in the first post). One gun and no gun for secondary. You have shot the primary gun to depletion (no ammo), now you want to pick up an enemy's gun and keep your secondary empty. This is impossible as it will not switch the gun, simply picks it up and takes it as your secondary since you do not have one. Now you have two guns, one is empty and one is your secondary, and have officially lost the empty secondary option. Let's say the only gun available at the time is the heaviest possible gun in the game, now you are unable to switch to empty gun hand and run fast for maneuverability. Whereas, if you could drop the initial gun you would remain as flexible as you began.
This would also be possible if when your secondary was empty, it didn't auto fill your secondary spot but switch your primary weapon as normal if that is what's in your hands at the time. Ex. MP7/B23R you can switch to the B23R and pickup another weapon without it removing your MP7 but if that hand is empty it auto fills that empty hand with the weapon.
Another scenario would be that you have two guns, blasted one to empty. But what is the point of being forced to keep an empty gun until you replace it with another gun? Why not just drop it and use the knife?