Azuth from FR might be a candidate. He is not a god of magic, but of wizards, and is mostly interested in the structured study of magic. From wikipedia:
The clerics of Azuth teach wisdom and restraint. This means that Azuth is often not the favoured god of sorcerers with their fiery, instinctual use of magic, and bards with their somewhat fanciful approach to it.
From the 3e FR Campaign Setting, the first sentence for Azuthian dogma:
Reason is the best way to approach magic, and magic can be examined and reduced to its component parts through study and meditation.
Likewise, quoting from the Sword Coast Adventurer's Guide (SCAG):
Azuth is god of a wizard's long hours of study, exacting standards of movement and speech, and cramped, ink-stained fingers.
Your cult might have decided that pact magic is an affront to the real teachings of Azuth, essentially a cheat to gain power without real work, swapping sweat with stolen power; without a proper understanding of what is going on. Warlocks could be seen as fools who are endangering the society with their broken understanding. Moreover, since the common folk cannot necessarily distinguish between actual wizards and warlocks, pact magic users will eventually cause serious paranoia within the society against reputable practitioners of magic, ie. wizards, as well.
Also according to SCAG, there are few dedicated centers of Azuth worship, and this fact might play well in your game. While there will be clergy who see this cult as heretics, they will be spread out and might not be able to mount a concerted argument to suppress the cult's "distorted" view of Azuthian principles. (An additional piece of lore information from 2e Faiths and Avatars: 45% of the titled clergy within the church hierarchy used to be wizards. Given that the 5e pantheon is structured in almost the same way as the 2e&3e versions, I don't see any reason if you wanted to keep this ratio also in 5e.)
Finally, Azuth is LN, so the cultists could see themselves as principled saviours who are willing to make the hard decisions others are unable or unwilling to do. What they are doing is to maintain order for the greater good of the society. When witches/warlocks are captured, the cultists might offer them a chance to renounce their pacts, atone for the bad deeds they did under the taint of otherworldly patrons, and start a new life learning magic the proper way. You could even imagine multiclassed warlock/wizards who joined the cult this way and having been converted, they could be even more zealous than the others in the cult.
PS: Following a comment by KorvinStarmast, it might be worth mentioning that within the 5e rules, you might have one or more Arcana clerics of Azuth playing important roles in this cult, either openly or covertly. I can add that such clerics could even be of LE alignment; not only 5e allows it, but also as far back as the 2e, Azuthian church accepted LE clergy according to Faiths & Avatars.