The Greek Amphictyonic League was a religious organization that sparked a series of "Sacred Wars" in 596BC. This was less ideological in my mind than you are implying for the Crusades or similar. The issue here was that a city, Kirra, was taxing (or in the Amphictyonic League's mind, robbing) travelers on the way to Delphi who were to make offerings to the gods and recieve oracles. This war was notable for being the first instance of chemical warfare when the Leauge marched against Kirra's walls and poisoned their water supply in the process of laying siege to the city. The second and third Sacred Wars were sparked when the Phocians attempted to become masters of Delphi and then sacked it of it's treasures. The most useful corollary to what you are wanting is probably this. The Fourth Sacred War was declared when Amphissa cultivated land sacred to Apollo and the Macedonians crushed them in response (essentially leading to the domination of Phillip II over the whole of Greece). The last one is probably the most akin to a religious war in the sense you were speaking of since it was in direct response to someone profaning land sacred to a god.