I'm making a paladin of Iomedae her favored weapon is the longsword. One of the enhancements listed under divine bond is disruption. In the text for disruption (pg 347) it says it may only be applied to bludgeoning weapons. So is this waviered for paladins since there are several who's favored weapons are not bludgeoning? All the other abilities listed under the divine bond are useable on any weapon.
Well, your mileage may vary, but for me as a DM I don't see any reason not to have swords or spears of Disruption if someone wants to make them.
However, if I were to interpret the rules as written without applying my own biases and my own eagerness to right the rules wrongs, I would say that the correct interpretation is the list of weapon abilities under Divine Bond is just a generic list of available abilities that all paladins can choose from, but other restrictions still apply as noted in the descriptions of the individual Special Abilities.
In other words, if you're wielding a weapon that is not appropriate for some of the Special Abilities on the list, then those abilities are not available for you to use with that weapon. Change weapons, and you can use the Special Abilities, although it might be possible that other abilites on the list are now inappropriate for your new weapon.
And yes, I know, the weapon must be the deity's favored weapon, so changing weapons is not an easy option. But I'm allowing for the possibility that some deities might have more than one favored weapon, or the paladin might switch deities (not an easy task, but in the right campaign with the right quest, it might be possible), or maybe your deity's favored weapon is a double-weapon with different ends (so all you really have to do is use Divine Bond on the other end of the weapon).