I'm going to jump in on this and we'll see where the dust settles.
First, after reading the documents linked above, both sides are probably full of half truths. Maybe just a bit of sore grapes on Worlds part.
I'm willing to bet Sonair is going to do it for a lot less than World and have a lot more control. I assume World is making money on this operation, by up charging on FA's that make a lot more than Angolans FA's will, and a premium on the MD-11 lease, plus a markup on the pilots, maintenance and insurance.
Sonair will get two 747-400's that will have 0% stops in route, carry more, and if as good as Polar is doing, over 98% reliability, with a lot cheaper FA's, and a decrease in all other costs because of no markups.
As far as the integrated cockpit crew, we'll see. This is a lot different than World's situation and Atlas has made no public comments on the matter. I assume they have spoken to the union? The planes will not belong to Atlas. So the two planes will be added to the planes Atlas already operates. So this will be a gain to Atlas, whereas World letting an Angolan pilot on your planes would be at a loss in World pilot positions. Atlas doesn't have a FA union contract, so no issues there.
I see this as a plus for both Sonair and Atlas. Atlas gets into Pax operations, gaining experience for the time required prior to hauling Pax for the military, and recalling some furloughed pilots. Sonair will gain by running it for less than World was charging, gaining in the capability's of the 747, and more control.
As is the normal progression of things, at some point in the future, Sonair will probably be in a position to do the operation without Atlas as well.