Eliminating Carter and Jorge
Posted December 23rd 2011, extra method added on the 30th
Here's an excellent simple use of Jun's Falcon. After stealing the Falcon at rally point alpha, it's easy to get Carter and Jorge linked to it to get them left behind, allowing you to tackle the east valley and the battle outside the relay outpost without them cluttering up the place. They won't turn up again until the cutscene in the outpost. Aside from the welcome relief of being rid of two prime knuckleheads - always a good thing in my book - it means more killing for you, and more control over the various skirmishes. Yay! Details follow - plus an elimination method I found later which doesn't need the Falcon.
Going on foot
If you're not interested in taking the waiting truck, here's what to do. Down the Falcon, pick up Carter and Jorge, then dismount to continue the level. They'll stay with the Falcon. Carter will switch to the pilot's seat once you get about 35 metres away, but won't actually take off.
Taking the truck
If you're going to want the truck, you have to be careful that when you board it to head into the valley, you're not close enough to the Falcon to tempt Carter and Jorge your way, breaking their link to it. You need to be at least 49 metres away to be safe; approximately the distance of a full sprint. The simplest way of doing things is as follows. Down the Falcon and drive to it. Pick up Carter and Jorge in the Falcon and land back up the hill at least 49 metres from the truck, then dismount and head for the truck to continue the level. As before, Carter will take the pilot's seat but won't take off.
Here's another way of working things. Down the Falcon and run to it. Pick up Carter and Jorge in it and head back over the drop which led to the rally point. There's a brief freeze while the area is reloaded. Land at least several metres back past the drop, then dismount and head for the truck to continue the level. When you get clear, Carter will start to fly the Falcon and attack any Elites left in the field, but that whole area will get unloaded before you're out into the valley proper.
Getting a handy checkpoint
If you want a checkpoint prior to your solo tackling of the valley, you can get one by finishing off the Elites you bypassed just before rally point alpha, if any are left. I'd suggest doing it with the Falcon, having picked up Carter and Jorge. After that, you can simply leave the Falcon in the field. As long as it's at least several metres from the drop, you'll be able to board the truck if you want, without attracting Carter and Jorge.
Truck retreat method
A week later I've found a way of eliminating Carter and Jorge from the valley without using Jun's Falcon. At rally point alpha, get them aboard the truck and drive back into the field. Kill off any remaining covies. Have the truck a fair way into the field with Carter and Jorge aboard - as far as the hay bales will do - then dismount and run off. They'll usually get left behind (look back and check for stationary indicators when you get past rally point alpha), in which case they'll be absent throughout the valley. However, if you board a Falcon with Jun on which descends after the evac zone battle, they'll materialize on it for the trip to the relay outpost - right before your eyes.
Note: If you're going to want Jun's Falcon at rally point alpha, bring it down before going to the truck to pick up Carter and Jorge. If you go to the truck first, the Falcon will fly off and you won't be able to bring it down until some place deeper into the level.
I tried a variation of things in which I drove them back, got them out of the truck, then speeded off alone. However, even when I took them right back to the farmhouse, it didn't work; they materialized in the valley later. Apparently the truck needs to be left with them.