I ran into this exact situation when playing the 3.5e version in Pathfinder. Here's what I did to convert the Inquisitors:
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Inquisitor Class
(modified Cleric)
Skills
Lose access to Diplomacy and Heal as class skills. Gain Intimidate and Use Magic Device (see Inquisition Domain) as class skills.
Class Abilities
Replace Channel Energy with Rebuke Magic.
Rebuke Magic
You channel negative energy to create a disrupting effect towards magic. You may use a channel attempt as a dispel magic effect to counterspell. You must roll a 1d20 + your cleric level and beat a DC of 11 + the spellcaster's caster level.
You may channel energy in this manner a number of times per day equal to 3 + your Charisma modifier. You may gain extra uses through the Extra Channeling feat. Other channeling feats do not apply to this application of channel energy.
Gain Reactive Counterspell (from the campaign setting) as a bonus feat at 1st level.
Gain the Inquisition Domain. (Only one domain, however it has two strong abilities, and you still get two choices for Domain spells).
Inquisition Domain
Granted Powers
You are a hunter of spellcasters, and as such know much about disabling and using arcane magic. You gain Use Magic Device as a class skill, and gain a +1 bonus for every two cleric levels (minimum 1) to checks made to activate a spell completion item (such as a wand or scroll) that is arcane in nature.
Binding Touch (Sp): You can cause a living creature to become dazed for 1 round as a melee touch attack. Creatures with more Hit Dice than your cleric level are unaffected. You can use this ability a number of times per day equal to 3 + your Wisdom modifier.
Dispelling Touch (Sp): At 8th level, you can use a targeted dispel magic effect as a melee touch attack. You can use this ability once per day at 8th level and one additional time per day for every four cleric levels beyond 8th.
Spell Resistance (Sp): At 9th level, you gain spell resistance 12 + your cleric level for a number of rounds per day equal to half your cleric level. These rounds do not need to be used consecutively. Activating this ability is a free action that may be used in response to being affected by a spell, even one you were not aware was being cast.
Domain Spells 1st - detect chaos, identify; 2nd - arcane lock, zone of truth; 3rd - detect thoughts, dispel magic; 4th - discern lies, imbue with spell-like ability; 5th - spell resistance, true seeing; 6th - antimagic field, geas/quest; 7th - dictum, spell turning; 8th - protection from spells, shield of law; 9th - imprisonment, mage's disjunction
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