I rarely bother with pay guidelines. I look at the Johnson, the job, and what the Johnson reasonably would pay (or can afford to pay) for the job. A low lifestyle Johnson trying to get back at a gang that killed his wife in a drive by probably isn't going to be able to afford 50k. Meanwhile, a high lifestyle naive fashion designer looking for someone to investigate her partners death might not realize that 200k is far more than "standard pay."
That said, my runners don't have any qualms about turning down jobs they don't feel are worth it, but they know they aren't going to get a new job that night for turning it down. They usually will find their own work (fortunately I'm good at running on the fly, so when they turn down a run and decide to knock over a Weapons World truck, I can adapt quickly). If they don't come up with something, a few weeks pass in game and I pull another run out of my file. Fixers don't like setting up Johnsons with runners unwilling to work.
On another note, if you do want to run the standard, just figure up stats for the most powerful opponent. That's one baddie a run. That's only one enemy per run you have to stat out. You can even have generic stats to pull from for the big bad (in my folder I have, for example, Bad Ass Combat Troll). His highest dice pool is his close combat (Agility of 7 + Skill of 9 = 16 DP). That's enough to figure base pay if you want to use the book.
Don't worry about the runners going off target on a run. If they're getting paid to burn down a gang drug operation, they aren't going to get paid extra for wiping out the whole gang, so don't figure that in. Just figure in the actual run's data and everything else they are choosing to do for free effectively.
There is a reason a lot of the professionals won't pull the trigger on someone they aren't being paid to. It's a waste of time for them. Time is money.
Another thing to note is that the base pay of the run should rarely be the only way the runners are making money. All that extra shiney they can get their mitts on is fenceable. Yes they're being paid to burn down the gang's drug operation, but those guns the gangers had can be fenced for a bit of extra cash. If the Johnson didn't specify to dispose of the drugs (or the players don't mind a bit of backstabbing) the drugs could be sold off as well.
Many of the Season Two missions let the runners net more money from paydata and stolen goods than the actual base pay.
Of course, if the runners are really unscrupulous, they could be dragging bodies to their local body chopper and stripping used ware out (for sale or implantation).