It's a little more complex than religion vs. religion. That's a impoverished region, so there's a wave of American and European evangelical missionaries coming in that do things differently than the old-school Protestants and Catholics. It's as much a class war, as these missionaries looking for souls to win over tend to target the lower-caste segment of the population.
Some Hindu swami was assassinated in August which touched off the wave of violence. You've got Maoists claiming responsibility, but officials are blaming Christians, so there could be some political motivations as well.
Big mess though.
http://www.csmonitor.com/2005/0401/p01s04-wosc.html