I think it would depend on which AP you were playing. If you are playing Reign of Winter, I would suggest Desna, as most of the native clerics who oppose the witches in Irrisen are Desnan. For Iron Gods, I'm not sure. As Voltron64 suggested, Iomedae is a good bet, as she probably the most militant anti-evil goddess.
Yeah, I agree with Iomedae, in fact if you know someone who has Faiths & Philosophies, it has a really cool in-world Iomedae propaganda spread that's a spot on parody of how certain religions can be so anti-everyone else, but it I think would give you some good insight into being a witch hunter of Iomedae :D
Torag is an OK option, I'd think. LG god of the forge and protection. He's a dwarven patron and similar to Moradin for Golarion. I don't know him well enough to know about his paladins and inquisitors and such but as a protector with crafting he fits well with cutting edge black powder tech in my mind and being against supernatural evils.
Hmm i'd say if the character is a dwarf then Torag would be good, but Torag is really about protecting the dwarven people (or your people, for the humans that follow him)... whereas Iomedae's paladin code is alllll about killin bad stuff.
Spoiler:Iomedae The paladins of Iomedae are just and strong. Their
mission is to right wrongs and eliminate evil at its root.
They are crusaders and live for the joy of righteous battle.
They serve as examples to others, and their code demands
they protect the weak and innocent by eliminating sources
of oppression, rather than the symptoms. They may back
down or withdraw from a fight if they are overmatched,
but if their lives will buy time for others to escape, they
must give them. Their tenets include:
• I will learn the weight of my sword. Without my heart
to guide it, it is worthless—my strength is not in my
sword, but in my heart. If I lose my sword, I have lost a
tool. If I betray my heart, I have died.
• I will have faith in the Inheritor. I will channel her
strength through my body. I will shine in her legion,
and I will not tarnish her glory through base actions.
• I am the first into battle, and the last to leave it.
• I will not be taken prisoner by my free will. I will not
surrender those under my command.
• I will never abandon a companion, though I will honor
sacrifice freely given.
• I will guard the honor of my fellows, both in thought
and deed, and I will have faith in them.
• When in doubt, I may force my enemies to surrender,
but I am responsible for their lives.
• I will never refuse a challenge from an equal. I will give
honor to worthy enemies, and contempt to the rest.
• I will suffer death before dishonor.
• I will be temperate in my actions and moderate in my
behavior. I will strive to emulate Iomedae's perfection.
While an inquisitor wouldn't be beholden to the Paladin's code, it's still a good idea of what Iomedae expects of her paladins, an inquisitor should at least try to live up to that when he can.