A lot of mentions of conjury and white magic specifically reference "purifying aether". In a world where aether is scientifically "magic" and "soul", spiritual (aetheric) forms of pollution are very real, so spiritual (aetheric) forms of counteracting that are also very real. (Gridania takes heavily after pre-Buddhism Shinto; so thanks for bringing that up Sanna.) It might not be more complicated than that; "purified" things are simply restored to their natural, balanced, benign natural way of being, as opposed to being in a state of "corrupted/tainted" disturbance of that order.