Priffe, you ask what is surely a rhetorical question "How can the South ever be stable when Alger lets the madness continue?" A question which I am sure you will agree, many will have asked since April 2003 - an important datum for this region.
The Tlemcen Mafia run a kleptocratic business based upon hydrocarbons and other natural resources with no need for tourism or evolved democracy. There is a less rhetorical question with which I know you are familiar which is why there should be more leniency in Djanet? This is likely closer to the current bearded baddies - possibly holed up just next door in the Acacus of Libya.
Personally, I tend to subscribe to the hypotheses of Keenan et al; that it suits Algiers to have some instability and that they fine-tune this from time to time. Enough trouble further south and the Red Zone is relaxed. If peace breaks out in Azawad - don't hold your breath - a new El Para, MBM, or Abou Zeid will surely emerge and reach for the Cemtex and Kalashnikovs. And so we go around.
The South, the Sahara, like all Africa and indeed the populated world is a game of musical chairs. Business has to go somewhere; if unrest breaks out in A, the trade will go to B, and terrorists to C. Pass the parcel!
I also firmly believe - although some will scoff and call it imaginative at best - that since the N1 & Reggane routes were closed, and all the traffic went to the Atlantic, Bouteflika has still wanted a route to the Atlantic himself. And that this is far more important than any trade down to Kano, Logos, Ouga' etc. Hence the recent announcement regarding the Bir Mogrein route. Far easier to get the Chinese to upgrade a railway than build a new one, and "voila" minerals from Tanezrouft, Hoggar, and Tademait can quickly be on their way to China, America, etc. C'est facile comme ca
I am thankful I have visited Le Grande Sud as many times as I have and would always encourage others to visit, especially Djabbaren & Sefar, Tadrart, or Ahnet. But there are so many wonderful places in the Sahara, and indeed in Algeria, who knows how much wonderful Rock Art is yet to be discovered and catalogued in Mauritania, for example, where independent travel is currently easier? Who will be the new Lhotse of the C21st?
Sun is shining, no rain in Oxford, time to work on my Troopy!

Salaam
Budric / Zoubir