I think adding a simple "Do you really want to do this"- prompt would be simple, but it might bug people.
maybe we could instead use this to add a bit of extra functionality?
perhaps clicking "ok" here could send you to a screen where you can once again re-arrange your soldiers (like in the basescape, where you can change the order of soldiers in the transport craft)? from this screen, you would have two buttons: "start mission" and "back to inventory".