This is an interesting idea, but I'm not sure of the feasibility. Wouldn't the salt water lake simply keep increasing in salinity as the water evaporated? I know that desalination is mentioned in the article, but it's unlikely to be efficient solution to this since it is either very expensive to build (reverse osmosis) or requires lots of input energy.
Also, salt water is more corrosive so pipeline components probably won't last as long changing the economics of the project.
If there's constant evaporation which drives the inflow, wouldn't the new sea and the surrounding soil become very salty, like several large-scale dam-projects?
The problems of the Salton Sea are largely caused by the intensive agriculture of the surrounding watershed combined with the tendency in the past 40 years to horribly overuse fertilizers and pesticides (it turns out that agriculture is just as bad a polluter as industry, but it's more diffuse and thus harder to target with regulations. Also, the farming lobby is probably the most well-protected in politics). If Qattara avoided such fertilizer practices, it could probably avoid such a fate.
On the other hand, I'm more worried about the sustainability of aquifer withdrawals. The Nubian aquifer hasn't had significant recharge for thousands of years. As Ogallala shows, "a lot of water" is not the same as "limitless water" (some of the aquifer in Texas has completely run dry).
Also, salt water is more corrosive so pipeline components probably won't last as long changing the economics of the project.