It's been about a year since I looked at information on East Timor, so I researched it at these links, among others I found less useful:
http://news.bbc.co.uk/1/hi/world/asia-pacific/503050.stm I actually found this BBC link to be the most clear overview.
http://www.un.org/peace/etimor/UntaetB.htm I posted this because you seem to favor the UN perspective. I find the UN to generally favor Muslim and other anti-American/anti-European interests. Where brutal third-world dictatorships voice strenuous objection to relatively minor violations of more civilized nations, while they slaaughter and brutalize their own citizens and minorities. Sudan, for example.
http://www.globalissues.org/Geopolitics/EastTimor.asp Just a third source, which I also found to be a good overview of East Timor.
None of these sources mention that East Timor is Catholic, and that the invading Indonesia is Muslim. But I think we both know that's an influential factor.
The BBC link acknowledges that East Timor's independence represents a threatening presence of Europe in their region. But since the citizens of Timor are natives of the region, it is arguably East Timor's ties to European culture, and specifically Christianity, that Indonesia finds threatening.
I found this overview of the clash of Islam and Christianity particularly relevant to this discussion:
http://www.700club.com/cbnnews/commentary/islamhistory0212%2Easp It discusses in detail the events leading up to "Christian aggression" in the Crusades, detailing 400 years of Islamic brutality toward Christians in Jerusalem and the surrounding area.
I know you have an aversion to Christian sources, but there are few places these events would be given fair treatment elsewhere in the media.
There is a tendency to overplay Christian aggression, and downplay Islamic violence and aggression.
