There are no rules for weapons being selected from the armoury replacing existing weaponry on a character. That said PEOPLE DO IT ALL THE TIME.
For example, Ork Nobs in Slugga Mobs come with a Choppa and Slugga. Every player gives the Nob a Power klaw, replacing the Choppa even though the rules don't specifically allow such a replacement to occur.
In short, everyone and their mom allows weapons to be discarded so that you can take other weapons. If you want to give your Chaplain Lightning Claws that is fine, he'll just have to leave the Crozius at home.
Again, none of this is RAW, but no one will ever give you a fuss about this so it might as well be.
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