Most SDN discussions about international work relate to pre-meds and med-students, this is an uncommon one discussing residency and beyond. I'd like to first say that I have no connection with MSF and can't comment on that group, their motivations or accomplishments. I can comment on the more general topic of residents, fellows, and attendings doing international medical work from many years of doing it and supervising it.
I certainly agree that it is best to be making grand political and economic changes to help people develop sustainable approaches to improving their health. However, the reality is that few American physicians have that type of connection with a foreign country/government and those who do generally have spent decades building up to that point. To indicate that only this type of work, or large public health projects is worth doing, is to, in my opinion, avoid doing anything. One is not obligated to get involved internationally, but to use dislike for one group, or belief that only national-scale projects are helpful, is not a fair reason to reject all projects.
It is also true that helping individuals, through small medical projects in tiny communities is frustrating, non-sustaining and can be seen, not incorrectly, as taking some of the responsibility away from the national government for providing these services. However, the overwhelming majority of such projects are done, in my experience, by very well meaning people and in areas that simply would not be served if they had not come. I am doubtful that the governments would or could take over these clinics, etc if the Americans and other Westerners left. As such, the treating of an individual, especially a child who cannot do much for themselves has a lot of intrinsic value and is unlikely to set back political, social or medical development. I can't speak for every community, but I have substantial doubts that most of the people assisted in these projects dislike the helpers. In fact, rather than thinking of us as colonialists, I believe the usual thought is that they believe we should be doing MORE to help them. But of course, YMMV.
However, just separating projects into big nationwide interventions and tiny individual ones denies the middle ground which I think is a growing and important one. The middle ground consists of development programs and partnerships between US institutions (or large groups) and foreign institutions. There are other such models, but, this is an important one. In this model, institutions commit to capacity building and training in ways that the local government could not. For example,
Harvard AIDS and similar programs involve fully-supported, sustainable training and care programs. There are larger and smaller such programs covering a range of conditions, institutions, etc in existence. Many focus on local capacity building.
So, whether you are interested in MSF or not, there are multiple opportunities to participate both during residency and as an attending in projects that have some sustainable component.