So you want an actually holy sword or evil sword?
For your clerical NPC enchanters:
Puissance (Holy) - This enchantment is functionally the same as Magery-based Puissance, except it is unaffected by No Mana Zones. In addition, its bonuses do not apply in combat against good creatures or inanimate objects. Normal animals, evil foes, etc. are affected normally. Weapons enchanted with Puissance (Holy) will detect as holy to anyone with any level of Holiness or Power Investiture on a Per+Holiness or Per+Power Investiture roll. In addition, Holy Puissance will give its bonus to any roll for True Faith with Turning, if the weapon is presented boldly while concentrating.
Puissance (Unholy) is identical, except its bonuses apply against all opponents, good and evil, animate and inanimate, alike. It is affected negatively by Sanctity on a 1-for-1 basis (An Unholy Puissance +1 weapon is +0 in High Sanctity areas, a Puissance +2 weapon is +1, but would be +0 in Very High Sanctity areas *). Optionally, bearers of such weapons cannot use them to directly harm the truly good or innocent.
Holy and Unholy Accuracy are logical extensions of this, and would work the same way - evil vs. everyone, but affected by sanctity, while Holy is only vs. living foes, either unaligned or malign, but not versus fellow holy types.
The idea here is that Holy weapons aren't especially good at smashing up physical objects and can't hurt good people (well, can't hurt them extra, anyway). They shine through even in evil Unholy sanctuaries, though, and show up as Holy when see. Crusader types can present their weapons as they turn the undead. And the usual shields against magic don't apply here.
Cost on these is double that of the normal enchantment (double the energy cost, then calculate the price), and in general churches will only enchant such weapons for the faithful. Evil types might be more free with it, but in general would be greedy and unpleasant types to deal with, and using such weapons would mark you as a tool of evil. Not good, in most game worlds, and perhaps a good excuse to pick up Social Stigma (Excommunicated)!
* I re-wrote this to use level names, not shorthand for level changes like I did originally. You could also go with Power levels, which would, in general, mean Unholy Puissance at Power 15 does nothing in a High Sanctity/Low Unholy Sanctity area. Or you could just go ahead and say that Unholy Puissance +1 or +2 do not function at all in High or Very High sanctity holy areas, and that Unholy Puissance +3 is reduced to +1 in High and does not function in Very High. You shouldn't be able to march around into the high holiest sanctuaries with evil stuff and have it not be affected, but "bring your blessed blade to clear out the temple to Hell" makes perfect sense. Corruption is turned away by good, not matter if it comes to the good or the good comes to it.