Current plan of action is to put the whole game and every mission up on Steam, and update the install whenever there's a new mission or game update. The alternative is to do as you say.
I think missions should be downloaded within the game with the downloader. If you ship them all everyone has to download everything, even if they already played the mission or just don't want to play that specific mission at all. Keep things small and simple. In my humble opinion download the core dark mod from steam (including updates) and download the missions within the game is the way to go.
Edit: If new missions are available you can also announce them on the community hub to let people know about them.
Edited by LordSavage, 12 March 2015 - 07:30 AM.