Sqd, the Church did indeed march behind the army during the Imperial wars, as a point of fact the Boxer Rebellion (or Boxer Uprising, take ya pick) was a violent reaction to the spread of Christianity in China and especially the so called "Rice Christians" we also invaded a sovreign (neutral) country Iran in 1941 (Operation Countenance), India had a whole new govermental system imposed upon it as did Malaya which survive to this day.
This riot in China HAS NOTHING TO DO WITH RELIGION, it is a race riot.
The Uighur feel (in some ways rightly) that they are discriminated against, they feel that they are not afforded the full protection of the law and are often the recipients of undue and unfair attention off the police.
There are historical cultural reasons for this (see Julnar's question below) are well known, these attitudes were not a problem until the economic diaspora as a result of reform and opening.
The great leaps forward (couldn't resist that) in China's infrastructure has also allowed inward investment from other areas of China, which can cause resentment and envy in the region.
Malaysia had a bout of very violent anti Chinese riots about 10 years ago, it's nothing new or unusual.