I agree 100% that it is odd and jarring that the clerics hand out bastard swords. Especially if it's particularly sacred to their god.
Granted, it's a bit of an assembly line in practice, but in theory the results of handing in commendations is a reward to an extra-planar stranger who went "above and beyond" to help the residents of Eveningstar.
What kind of gratitude would it be when an adventurer has stopped evil necromancers from violating the graves of relatives of the clerics, rescued hostages held by a drow priestess, possibly de-poisoned the water supply for the whole town, rescued the (eventual) savior-ess of the entire realm multiple times, and even helped in myriad "little" ways in the King's Forest, to be told "It's a violation of your god's tenets to use a sword? Bah...go bother the villagers, they might have a stick for you."
That's not to say that the clerics would be expected to have every possible cleric weapon choice. But they should have a "simple" weapon available (since all faiths can use them) to give as a reward to exceptional heroes passing through.
edit: Also, religious of any faith do NOT pass out cherished symbols of their god to non-believers. Quite the opposite would be true. They would have something on hand to give to the hero that saved Eveningstar (and Faerun). But they would not give away magic items normally reserved for the greatest champions of the faith. Even if the main temple sent them a full crate.