First of all, beware of Book of Exalted Deeds, it can be quite broken (Saint, in particular), especially if the role-play requirements are not enforced.
With that being said, the Calling (Su) and Conversion (Su) class features of the Emissary of Barachiel are simply impossible to save against, seeing as they pit a Diplomacy check versus a Will save: it is just much easier to boost a skill check than it is to boost a save.
On the other hand:
An Emissary can use this ability once per day per class level, spending a full-round action to issue the call.
Humanoid creatures within 30 feet of the Emissary are potentially affected.
Calling is an Enchantment (Compulsion) [Language-Dependent, Mind-Affecting] effect.
And thus given the wording of the Conversion (Su) ability, I will assume that it is too.
This has several implications:
A Full-Round action occupies a whole turn, which generally precludes any other Move/Standard action.
The range is short, any creature further away (archers, casters) is unaffected.
Only Humanoid are affected, thereby a strict reading could exclude Monstrous Humanoid which can make the bulk of your foes. Giant, Fey and Undead are also a category of their own, and there are LA +0 templates to turn into Fey or Undead.
The effect is powerless unless the foe understands the Emissary. That is, unless the Emissary speaks the foe's language OR uses a spell to be understood, the ability has no effect.
The effect is likely powerless unless the foe hears the Emissary, a deaf foe, or a foe in a zone of Silence, cannot hear the Emissary. For example, casting Silence on a pebble and slipping it into the Emissary's pocket undetected...
The effect is powerless against creatures immune to Enchantment or Mind-Affecting effects (though I am not sure if any Humanoid race is immune).
Conversion (Su) is acquired at ECL 8 at the soonest, by then intelligent foes should have some generic counters for Enchantment or Mind-Affecting effects as those are nasty effects you really don't want to succumb to. Check the List of Necessary Magic Items to equip your NPCs, in this case: the 1st-level spell Protection From Good suppresses the effects of Enchantment (Compulsion) for its duration (1 min/lvl).
All in all, using Calling (Su) or Conversion (Su) seems like a good way to waste a full-round action in the middle of combat.
Also, out of combat, someone who gains a reputation for bullying others into helping him may easily be barred from the nobles mansions/king's court/etc... Coercion has social consequences, see the rules on the use of Intimidate.