Award them at the end of the run
Being outclassed or not, usually the payment is agreed before the job is taken, considering the point of view of the contractor (the Mr. Johnson). He could pay extra after the job is done with proper negotiation or if he is told that things werent as he was expecting before (during the job offer) they took the job, and thus, they require compensantion for the trouble.
If the job was to simply escort someone out of the airport for a few hours until they arrive at the corp's safe zone, what the runners will agree and negotiate upon will be that job. For the sake of the example, let's say they agreed to do this job for 10,000 nuyen (split among them, it's an "easy job").
Of course, things never go as planned, and what the Mr. Johnson wasn't expecting (or maybe he was, that's why freelancers were hired) was that this guy was being targeted by a rival corp who are interested to hire him (whether he wants the job or not). So, the runners will face a lot of resistance while transporting him back to the safe zone, exploding vehicles, killing hired guns, taking a few bullets, and spending lots of ammo.
Once finished, they contact their fixer to inform that the job is done, and tell him that things didn't go as planned and they faced a lot of issues that the Mr. Johnson didn't mention on their job interview. Or, the runners contact the Mr. Johnson directly and tell him all this (depends on how your group does it).
Then, now that both sides know about the specifics of the run, the GM might allow a second round of negotiations, where they might try to obtain a higher payment for the job, or the Mr. Johnson realizes the job wasn't what he was expecting, sympathizes with the runners, afterall, he was expeting trouble but not that amount of trouble, and offers a better payment.
As a GM, of course, you knew this all the time, and when designing the mission, you already fixed a payment value based on the real difficulty of this mission, following the guidelines on the Core Rulebook (page 375, Run Rewards).
Now back to our example, they were offered initially 10,000 payment for this job, which should be 2,500 per runner on a group of four (this is the initial cash). Checking the highest dice pool they will have to roll against (15 for the elite hired guns), the multiplier is 3 (15/4, rounded down), or about 7,500 per runner. This, of course, doesn't take into account other issues that could increase the multiplier, as seen on the guidelines (like exposure, being outmatched, facing lots of spirits, etc).
Unless the GM is making up the mission on the fly, he should know this value already before they even take the job. On published missions, the initial value is usually different from the actual payment, extras are awarded at the end of the mission that increase the total payment for the job. Simply have this in mind and plan accordingly.
The book does not mention what should happen in case the mission is different from what was agreed on. But as a GM you can plan ahead and make the proper adjustments on the reward. Negotiations should increase the initial value (3,000 by the book) by 100 nuyen per net hit on this check. If the final value for this mission was the triple of that, also increase the difference by three times, or 300 nuyen per net hit on the Negotiation check at the end of the mission.
On our example, they agreed on a 2,500 payment (with an extra 100 nuyen per net hit on negotiations), but the reward calculations were 7,500. Simply make the Mr. Johnson pay an extra 5,000 nuyen (with an extra 200 nuyen per net hit on negotiation) for a job well done. The runners will take this as an extra payment that tripled what they agreed on and will return home happy with the outcome.