Old English halig "holy, consecrated, sacred; godly; ecclesiastical," from Proto-Germanic *hailaga- (source also of Old Norse heilagr, Danish hellig, Old Frisian helich "holy," Old Saxon helag, Middle Dutch helich, Old High German heilag, German heilig, Gothic hailags "holy"), from PIE *kailo- "whole, uninjured" (see health). Adopted at conversion for Latin sanctus.
Primary (pre-Christian) meaning is not possible to determine, but probably it was "that must be preserved whole or intact, that cannot be transgressed or violated," and connected with Old English hal (see health) and Old High German heil "health, happiness, good luck" (source of the German salutation Heil). Holy water was in Old English.
Holy has been used as an intensifying word from 1837; in expletives since 1880s (such as holy smoke, 1883, holy mackerel, 1876, holy cow, 1914, holy moly etc.), most of them euphemisms for holy Christ or holy Moses. Holy Ghost was in Old English (in Middle English often written as one word). Holy League is used of various European alliances; the Holy Alliance was that formed personally by the sovereigns of Russia, Austria, and Prussia in 1815; it ended in 1830.