Have you read the White Man's Burden? (the book) I'm not sure you are qualified to say it isn't fair to bring it up if not, as it deals exactly with this. (and yes it isn't about race, nor is the book, but about how broken the approach to aid has been in Africa in particular)
And yes, indeed, bringing small local NGOs to help one local community can be more harmful than not. Among other reasons because you are only adding to the fragmentation of health care services in a country that is desperately trying to unify them and just seeding confusion within that system.
EMR's like what it looks like Watsi is doing have been going on since before I was there in 2007 and like I said are constantly popping up because everybody is like "hey, I can build an EMR". That should be the first clue that it isn't the core problem at hand.