Cyberdiscs are notorious for their high reactions, toughness, and tremendous damage and good accuracy. You can deal with them camping your craft exit in at least two ways:
1.) move tough and/or expendable units into their line of fire to drain their time units, then move in the ones that have the power to kill
2.) drop smoke in front of the craft before you step out, and use the smoke as cover until you come at them head on and get mutual surprise
Generally speaking, a crashed terror ship is easier to assault and gives you more points than a successful terror mission, however there are exceptions such as the situation you described with cyberdiscs getting in a rough ambush point, or getting lucky in a terror site and saving a lot more civilians than you lose. I will always take the crash if there are no other considerations, but shooting down the terror ship can be the hard part--though they go down pretty easy with avalanches in vanilla.