The funny thing is that there are few settings with only one religion (or at least with only one powerful supernatural entity willing to grant favors, even Christian mythology has referred to witches who get favors from darker powers). I think if we are going into a numeric system, having a few different gods or factions of gods that offer boons to their followers.
Ways to change prayer point values:
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Praying or sacrificing to a faction increases points in that faction, but can decrease points in opposing factions (and slightly in neutral factions as the gods get jealous, but probably only down to neutrality)
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Breaking a religious taboo decreases your status in that faction
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Certain other actions can help certain factions, but they might be taboo to other factions
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Completing special quests could grant big bonuses
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Asking for more favors than your level of piety allows gives a chance of having the favor granted, getting it granted at the cost of standing, or just getting smacked down by your deity for your insolence.
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Devoting yourself as a cleric of one god opens up more advanced levels but caps advancement in other tracks.
This is more of a game mechanic than an alignment system. Now some might take a balanced approach to keep all the gods happy, maybe sacrifice an extra goat to the sea god before a sea-adventure for an edge. A cleric or paladin would necessarily have to devout more resources to one or maybe a closely aligned group of deities/factions, allowing great boons and miracles in their domain, but a generally icy reaction from some of the other gods as they will alienate .