No, not really. East Timor is mostly Catholic. There are small numbers of Moslems, and some of those may be causing some problems, taking advantage of the instability, but this started with nearly half the East Timorese Army - and that is nearly all Catholic.
Yeah, I don't think there's any religious issue here. The only religious angle perhaps the fact that Mari Alkatiri is a Muslim prime-minister in a pre-dominantly catholic country .