Dunno if there is a way to stop a country from "defecting" once the wheels start turning, I seem to recall you can delay it at the recon stage. Cleaning out a UFO doesn't really do anything to the mission the aliens are performing except to give you points and loot.
Nope, can't be done - the transport needs to go back to base to refuel before it can go to another site. Can be done in Xenonauts though which is really nice.
Not sure offhand anymore, but it sounds correct. Pretty sure stunned aliens are placed in AC immediately after a mission so the same should be true for loot.