Favored weapons has become more and more watered down. The primary class that was intended to benefit from it. FvS, now gets less than the paladin. Universal trees like Inquis allow paladins to duel wield crossbows as favored weapons, but myself, a loyal servant of my deity (Paladin) is not able to convince him that I need to use a bastard sword, dwarven war axe, or even a longbow (even though you added a bunch of ranged multi-selects).
I really shouldn't be choosing my religion based upon what weapon I get, it is like choosing a church based on who has the best crackers. If a PDK can have a favored bastard sword, it really isn't a question of being OP. I think Holy Sword should make any weapon a Favored one in the hands of the caster - this includes shields, if not at level 14 - when you get the spell- at least with the kotc capstone. I don't want to go down the rathole of why someone with a shield isn't allowed to do decent damage in a game that has degraded into a system where success is indicated by your ability to kill stuff fast. If you think a shield makes you unkillable, you'd all have one right?
You clearly knew this was going to be a problem with these changes, given you added Search the Soul. So, for two feat changes, we can switch but probably not to Helm if a grew up on Eberron. This is assuming its not bugged. Why not save yourself some unnecessary complication and potential future bugs because it is just plain weird and unlike anything else in the game, and take the obvious choice of making Holy Sword reflect the deity's faith in the players weapon choices?
Reference: patch notes Search the Soul -
Characters with at least 6 Divine levels can now take a new feat in place of the Active feat related to their Deity: "Search the Soul: You are seeking guidance to new paths of Faith. Passive: You gain +3 to the Concentration skill. As this Feat has no particular required Deity, while you have this feat (and assuming you meet all other requirements), you can exchange your Deity with a Feat Exchange (using normal Feat Exchange rules and costs).