I think for the German language, I would go with an imperative case (as in giving an order) In German, as in English, the "you" subject is implied.
"Reinig mit Feuer" or "Reinig mit Brand" (both mean "Cleanse with fire") or "Reinig mit Flammen" ("cleanse with flames") or "Reinig in Flammen" (Purify in flames)
Reinigen is the verb for to cleanse, purge, or purify. Läutern is another verb that can be used for purify, clean, or reform
"Bestraf mit Feuer" (punish with fire) wouldn't be a bad idea either.
If you had a particularly bad problem with Skaven then I would suggest, "Mit Flammen rotte aus!" or "Rotte mit Flammen aus!" With flames, exterminate"
Now, since this is more religious in nature, you could add the adjective for holy, "heilig." For example, "Reinig in heilige Flammen" (purify in holy flames)