Generally, I'd allow a little bit of leniency when it comes to Prestige Classes that require you to have proficiency with, or feats related to, your deity's favored weapon (such as the Divine Champion).
For instance, I'd probably allow a Divine Champion of Helm to use a Long Sword, Bastard Sword, or possibly even a Greatsword to represent Helm's favored weapon, as long as the player has a good reason. They are essentially the same, only bigger versions of each other.
**I wouldn't apply this to the War domain or any spells, such as "Weapon of the Deity", which relate to your deity's favored weapon. These are very specific already.**
As it is, some of the deities in the FRCS have more than one favored weapon, such as Gargauth (dagger or throwing dagger), Lathander (light or heavy mace), Talos (longspear, shortspear, or halfspear), or Urogalan (any flail). These weapons are close enough to each other for it to make sense.
Also, you have to consider size. A Halfling Paladin of Torm, whose favored weapon is the greatsword, would probably only use a longsword. A Gnome Cleric/Rogue of Mask, whose favored weapon is a longsword, might use a shortsword instead.
Keep in mind that a Cleric or Paladin isn't required to use their deity's favored weapon. Mainly, these are for flavor, for use with the War domain, and for spells related to your deity's favored weapon.