Would this mean that the military secret project storyline would be over ? I was not too sure where it could possibly go myself.

That might be one option, at least eventually. Or first they might be offered the opportunity to keep working on it under ultra-classified conditions that might involve something like moving to the desert like Raj semi-teased Howard about earlier. So they have an episode or three were the guys decide whether they want to keep exploring high-level science at the expense of having to leave their wives/GFs behind. Or maybe they could come along but Bernadette would lose her career, Penny would be relieved about not selling drugs any more, but neither of them would have lots of clothes stores to shop at (which wouldn't be an issue for Amy).