Dude, that article says they "Might have some ties with Al Qaeda".
In reality, that group was the spiritual predecessor of Al Qaeda, before it took an Arabic name in order to honor the recently recruited and brainwashed rich-ass Arabs (including Bin Laden, who was one of the first) with their limitless finds to help their organisation.
The thing is there has always been such groups in the Northern postions of the India subcontinient/Central Asia, even thousands of years predating both Islam and Christianity. This ridiculously violent, brutal and savage mentality is what has preserved their cultural identity for thousands of years from countless invaders. Ironically, they used this same type of campaign against Muslims at one time - notably the Mughals and even later the Mongols after they in turn converted to Islam. They would throw the bodies of the soldiers in the rivers, so that they may flow downstream to their native lands and discourage more from coming.
They since adopted the foriegn religion Islam as all surrounding lands did so, and changed many teachings to be compatible or reflect this culture of theirs. That is why you see each child there know how to read perfectly the Quran - even adding special pronounciations which are absent or unheard of at the time it was written - yet they don't understand a word of Arabic, or the much more difficult Ancient Southern Arabic of the Quran.
They are viewing the Christians as being a tool of Westernisation - with their European-style Church buildings and sitting on chairs rather than the floor. Christians there are also culturally very Western, and would opt for Westernised clothing rather than traditional Saris etc...
This is just background, but in my personal opinion, I think Christians there should (at least on the outside) not look overly Westernised, and maybe build Churches like a traditional building there, but with a massive cross at the top r something. That way, they'll be much safer.
Also, who knows, maybe they'll all slowly adopt Christianity, and change it to align with their culture - so they'll be burnng Mosques and beheading Muslims on YouTube. :1orglaugh