In 1999 East Timor was occupied by Indonesia (a key ally of the USA in the area). It has since achieved independence, a process in which Indonesian government- sponsored militias caused untold violence, in which almost a third of the population were killed or starved to death. Many others were forcibly detained for years in Indonesian West Timor, having crossed the border as refugees.

The retaliation against people who support rebels has stopped, because the rebels have won. The Indonesian government is still in power in the remainder of the country, but they are now acting against Moslem separatists, and hunting the Bali bombers, so they can be forgiven for attempted genocide now, can't they?

Even given the probability that Allan C's allegation is true (names, dates and places would help- Google doesn't), as bad and worse were happening to the rest of the (non- missionary) population, so they can scarcely have been singled out for persecution.