lis,
I lived in Bali (would go back tomorrow if we could!) My hubby is Balinese.
I was living nin Bali til about 25wks into my pregnancy with DD#1, I was mostly in a village & not at nice airconditioned hotel & I managed...
I also eat where the locals eat & have never been ill..
Unless your planning on trecking in the jungles Malaria is fairly uncommon in the tourist areas, I know of many persons travelling, living etc in Indonesia who are, have & were preg without any issues.
If you eat at restaurants in the Tourist areas you should have no probs whatsoever, as these all have to abide by the Government regulations in regards to hygiene, food handling etc.
If you need any more info just ask, but there is no reason that asia is dangerous to travel in whilst preg, after all they make babies too....