I don't think any houserule is needed. There is nothing in the rules that forces you to make a fighter card for every weapon in a fighter's personal 'inventory', is it? RAW, I think you can purchase an Enforcer (it comes with a 'free' stub gun), buy them a Boltgun and 2 Shock Staves, and make them one fighter card that uses the boltgun and the shock staves. The stub gun would then just sit there in their inventory and gather dust.But doing that you had to houserule as well, otherwise under the random selection rule you'll have more profile to pick : 1 with only a stub gun, and one you'd want to use,
Now, if you do make them a fighter card using the stub gun, I don't know if you are allowed to 'destroy' it at some point in the future. The rules simply don't cover this.