Another idea I had, and this is a little more daunting, is incorporating the Signs into the Witcher's class features. Looking at the Rune Knight as a model, let's see what we can do here:
Sign Combatant: Whenever you reach levels 1, 5, and 9, you gain access to two Signs. Activating a Sign costs 1 Spell Point and is a half action, and activating an Advanced Sign costs 2 Spell Points and is a full action. You must have access to a sign to acquire its advanced version.
Aard: Up to 3 adjacent opponents are hit by a Medium Bull Rush action, using your Athletics result.
Advanced Aard: All adjacent opponents are hit by a Huge Bull Rush action, using your Athletics result.
Igni: Characters and objects in a 15 ft. cone are hit for 1d4 fire damage [AP 5] per two caster levels. A Reflex save (DC 10+your Int modifier+Melee Combat feats) halves this damage.
Advanced Igni: One character or object in medium and all characters adjacent to the target are hit for 1d6 fire damage [AP 5] per two caster levels. A Reflex save (DC 10+your Int modifier+Melee Combat feats) halves this damage.
Quen: Until you perform an attack action, damage equal to 10 + caster level is absorbed harmlessly each round. This protection has no additional resistance of its own.
Advanced Quen: Until you perform an attack action, damage equal to 15 + caster level is absorbed harmlessly each round. This protection has no additional resistance of its own. In addition, any attacker who damages the protection suffers an equal amount of lethal damage.
Yrden: Choose an adjacent square. Any opponent that enters this square must make a Reflex save (DC 10+your Int modifier+number of Melee Combat feats) or suffer 1d4 subdual damage per two caster levels (rounded up). The square remains protected until the sign is triggered 3 times.
Advanced Yrden: Choose an adjacent square. Any opponent that enters this square must make a Reflex save (DC 10+your Int modifier+number of Melee Combat feats) or suffer 1d4 subdual damage per two caster levels (rounded up). If he fails the Will save against the Stress damage, he fails 2 saves instead. The square remains protected until the sign is triggered 5 times.
Axii: An opponent in Close Quarters is subject to a Taunt action using your Sense Motive result. If he fails this check, he must dedicate his next available action attacking your choice of any target adjacent to him. If he succeeds, he gains a +1 bonus to his next attack against you this combat. Once an opponent has resisted the Axii sign, it cannot be used against them for the remainder of the scene.
Advanced Axii: Three opponents in Close Quarters are subject to a Taunt action using your Sense Motive result. If any one opponent fails this check, he must dedicate his next available action attacking your choice of any target adjacent to him. If any one succeeds, he gains a +1 bonus to his next attack against you this combat. Once an opponent has resisted the Advanced Axii sign, it cannot be used against them for the remainder of the scene.
So...those didn't end up looking anything like the Rune Knight's runes, but it's important that, if used as a class feature, that it doesn't dominate their class advancement, since Witchers have other abilities they need to succeed, and Signs aren't all there is to being a Witcher. Any character who became a Witcher through the Mage class probably deserves the bonuses to caster level they receive, since they will have key weaknesses in melee combat in general, which will likely be the focus of the other class features.
About the setting...
Sidenote: I forgot ENTIRELY about the whole alchemical body training thing that they go through, so it might be appropriate to put it in as a Talent, depending on how late someone can actually undergo the change. Since I haven't read the books, I don't know, but the time-frame of that change essentially mandates its position as an Origin or Class.
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