The Feral Champion gets Sacred Damage on their claws
Rather than empowering a physical weapon, a feral champion grows claws as primary natural weapons on each hand. These claws deal damage as a warpriest’s sacred weapon and can be enhanced as such.
This ability alters sacred weapon and doesn't replace it. Can a Feral Champion still then apply its sacred damage to any weapon they have weapon focus with and/or is their deities favored weapon?
Maybe read the first sentence you quoted over and over again 7 or 8 times.
Spoilers. No.
I have read it multiple times trust me. It doesn't take away the rule regarding selecting a weapon with weapon focus, including a different natural attack (aka not a physical weapon)
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Rather than empowering a physical weapon, a feral champion grows claws as primary natural weapons on each hand.
These claws deal damage as a warpriest’s sacred weapon and can be enhanced as such.
This alters sacred weapon.
"Rather than" = "instead of", and nothing indicates this is in anyway optional (it states he grows claws, not that he 'may' or even 'can' grow claws).