Of course, there's a downside to everything and this observation may seem rather pedantic: the net effect is positive, right? Well, short-term it certainly is, and long-term it seems like it should be. When things get better, NGOs will trickle away slowly, and the economy will stabilize.
The real downside, though, is that the "when" in that last sentence is really an "if". If everything works according to plan, then the NGOs will have successfully improved the lives of northern Ugandans. On the other hand, if things turn ugly, a good 90% of the NGOs will have disappeared within 24 hours. (A well-organized NGO writes an escape plan before even moving in; a rich one even buys sat-phones for that very purpose, in case the cell phone network is unreliable.) So if the LRA returns (or another rebel group starts up), the land will again be unusable, the camps will again be overcrowded and horrible, and to top it all off, the local economy will be in a worse condition than it ever was before.
Can you really blame the NGOs for coming in? Of course not. Everybody wants to help, and help is desperately needed. But the situation here is precarious, to say the least.