So I'm in a bit of a pickle. Here's the situation:

The PC team has been tasked with subcontracting out a Shadowrunner team. They picked their hires from the standard book archetypes, selecting a capable assortment. After the PCs Johnsoned out the mission, their subcontracted team runs against the corporate target. At the end of the Run, the PCs have an effective ambush setup, and per instructions, plan to liquidate the subcontracted team. Easy-peasy.

Now, let's hit play. Lets look at how it REALLY goes down.

After the end of Johnsoning, the players take on the roles of the subcontracted team, and make the run themselves using a random draw from archetypes they hired. During the run, things will go horribly, horribly wrong. Even the newest of runners would recognize that they've been deliberately sold out and wouldn't be foolish enough to trust their Johnsons to meet up post-run. So, like any good runner, they'll fall back to their Survive, Evade, Resist, Escape plans. At the end of the run, the players resume their normal PCs and hunt their former-selves, the NPCed subcontracted team.

I'd like to individually reward players Karma for coming up with the most successful Survive, Evade, Resist, Escape plans. I'm kind of thinking of this as a game of "Kill Doctor Lucky", with the players having preprogramed their NPCs escape plan (this is a good group of seasoned SR gamers, so someone spilling the beans is unlikely).

My pickle is how to judge all of this, and keep it fair, fun and running smoothly.

So, I'm wondering. Have you ever played or GMed something similar? What worked (and what didn't)?
All suggestions welcome!

I'd suggest sequestering sections of the groups.

PC Group A goes against PC Group B's NPCs, and vice versa.

I would not play them back to back.

Put something in the middle that your main PC's will have to do. Something completely unrelated so that, hopefully, your players will forget exactly what they came up with as their alts.

Easy:
Player a plays characters 1 and 2
Player 2 plays characters 3 and 4
Simply have them hunt characters not played by themselves.
Basically, in the end, player a with Character 1 and 3 against Player 2 with characters 2 and 4.
Character 1 hunts 3 and Character 2 hunts 4.

Have some of the NPC's be favored sons of the exchange so you can add some random help at appropriate times.

I love the Kill Dr. Lucky idea. That really takes the idea from being a handicap to being a bonus to play. I'd say let each player on his own write up a set of defenses for each player of the party (I'm assuming the party has split up, since that's pretty standard with runners facing heat). You vet them to make sure they're reasonable, and put a twist on them. Each defense that trips up the party somehow gives the contributing player 1 karma.