The Global Army had shown its planning and plotting skills to allow a safe and silent departure.
Khan's lessons were a big deal in the Harbor and network as a whole, and the strict policy over the released information made them one of the period's hottest news. Their end would attract immense attention, and the Global Army used that to hide the departure.
Everything was ready after two weeks of constant preparations, so a private ride picked Khan up from the embassy in the middle of his last lesson. The Global Army had made the announcement, so the scientists still inside the building baited the public's attention, allowing Khan to reach the hangars unnoticed.
The scientists were partially aware of the situation and didn't mind their role in that ploy. They didn't have much choice in the matter either, so they played along and waited for the right time to leave the embassy to handle the reporters.