The solution to this problem is extremely simple but I don't think ANET has any reason to change the system because they want us to purchase templates to perform swaps. They could easily make it so that if you drag and drop the legendary item into your inventory it simply disables that legendary unlock for that one character/weapon and now it acts like the old setup. This soulbound copy would not be able to be broken down or stored anywhere other than on that one characters weapon slot or inventory (excluding shared inventory), in order to prevent people from spawning multiple copies and dual wielding one legendary.
This change would allow players to setup a few legendary weapons with the correct sigil / stat combo and then when playing the game perform weapon swaps from their inventory window instead of templates. Unfortunately there is no monetary reason for ANET to make this change, and this would de-incentivize some to buy templates.