Basically I wouldn't.
An explicit, gameable system that adds presumably power and new capability to the character for what is a series of hard to track and complex choices (faith) is incredibly hard to design.
Even a system of static bonuses (or uses for points) that you give the player points in by your own judgement (aka fiat) is problematic for metagaming reasons.
A much simpler and better answer is to give this player plot content related to their god.
Spend a bit of time researching historical saints and the circumstances of their lives - specifically, deific intervention in their lives, or supposed deific intervention in their lives (people writing about them long after their deaths made some assertions that are heavily contested by eg. respected theologians). There's all kinds of altered perceptions, predictions, warnings, direct contact by means of signs and portents, other people being given signs and portents related to the individual, etc that come up in many different religions.
You can use those as inspiration for the way in which this character's faith, and the resulting interest of their god, affects them. This will naturally be interesting to the player and interest is just as good as power bump most of the time. Perhaps flowers grow when they walk barefoot on soil, or water they bathe in becomes a sacred spring after they defy the followers of a god of death in a situation where they expect that to kill them (standing up to them while a prisoner, for example, where they are likely to just execute an uppity prisoner).
In effect, award faith points for his actions, and grant boons, but keep the entire process opaque - he does not know when his faith is going to be rewarded, or in what measure. Make the rewards semirandom if you have trouble deciding on them, roll a dice on a table or something - the god is granting boons but not necessarily deus ex machina style 'get out of jail' cards, which just reads as the DM wanting to help the party out, but rather random deific style things which the party can potentially make use of or not make use of. Perhaps they decide to lure the evil vampire to the sacred spring, and the barbarian tackles him into it and the water dissolves him like the wicked witch in The Wizard of Oz. Etc.
Likewise, allow things sometimes when he prays for them and they are in the sphere of his god. Perhaps he prays for a community's crops to recover from a blight and they do after he spends all night out there, but not immediately, so at first it's uncertain etc etc.
So effectively, just expand it narratively in scope and give mechanical bonuses but not explicit ones and ones that require potentially a bit of work from the party to make use of. That will likely be far more satisfying for the player, and the rest of the table, and for you.