True. At least half of it is. The US shouldn't really exist, or should at the very least be confined to its original boundaries in my opinion. They are a special case, however, given the fact that they have basically wiped out the native ethnicities and their country wasn't made up by an higher and lower peoples (And you said yourself in your post about East Timor), but since that is well in the past, as much as it pains me to nod, I accept their presence as a single sovereign entity. History is very important, because it means the cultures are gone and cannot be retrieved and enforced upon the majority of the present population. Such is the case of the USA, unlike Indonesia.
I would apply such an opinion on a myriad of countries. Spain castillianizes Galicians, Basques and Catalunians, therefore I am in favor of the independence of those countries. England did the same to Welsh and Scottish, therefore I am in favor of the independence of those countries. North Ireland is reportedly mostly inhabitted by Scottish, so a condominium between Scotland and Ireland would be a possible solution, in my point of view. France successfully did it to Occitans, Bretons and Burgundians (History again), therefore I accept that France remains with its current continental boundaries (Corsica shouldn't remain French, however.) India should desintegrate into a myriad of states, as should Pakistan (Baluchistan and Punjab/Khalistan pops up to my mind as the most blatant cases), China should lose most of its external territory (Xinjiang, Tibet, Inner Mongolia), it should not however, lose for instance Manchuria (Manchu culture), Yunnan (Ancient Di and other non-Han tribes which were assimilated), and finally, Guizhou, Hunan, Jiangxi, Fujian, Guangzhou Huainan and Guangxi, which were territories which originally were home to many non-Han ethnicities, gradually assimilated into the Chinese (Han) ethnicity, recognized by the old Chinese emperors as barbarians. Since this cultures have large and by been absorbed in the course of history, and their distinct culture lost, I can accept that they are legitimatly part of the country they belong to. Africa would be a very special case. Since many people of the same ethnicities have already have seperate histories by being part of different colonies, the whole of Africa would need to be re-drawed, by ethnical groups, divided by the colonial boundaries (As people from the same ethnicity in different ex-colonies speak different languages, and that might lead to conflict in a unitary state (See Belgium about language conflictuality). Well, you get my point about countries which are legitimate or not in my eyes.
Just to note that ever since I read "lesser people", I rejoiced at the fact that East-Timor is independent.
However true that may be, the fact is that multinationals don't force an authoritarian Indonesian government to make a refenrendum. Other countries do. That's why you don't see Xanana Gusmão or (Insert random rebel leader here) travelling abroad to meet multinational companies CEO's. They travel to meet world leaders.
I'm pretty sure you can say that to the tens of thousands that died during the Indonesian invasion (Which was the classical "We are invading simply because we want to." reason), as well as the tens of thousands of victims of Indonesian repression, as well as to the victims of
this incident.