Back in my day
Declining the Job
I try not to pick characters who won't do the job. A pacifist isn't good for wetwork, a tank isn't really suited for stealth, and if the character and the Johnson have some bad history, I won't take them unless there is a very good reason for them to be on the job. Of course, if you have objections after the meet, be that not enough money, some moral objection or any other reason, you're free to walk away from the job. Though there might be some form of repercussion for walking out on a job. Less so if you do it before agreeing to do the job, but there will certainly be times where it affects if a Johnson contacts you again.
Derailing the Run
If you want to work against the Johnson on a run, or do the job and get payment and then gank the sucker, then by all means, that option is available to you as a player. Sometimes the Johnson screws you over, sometimes the Johnson gets screwed. This is well known in the Shadowrunner's line of work. Of course it might affect you negatively even if you succeed. If you are going to try and change the parameters of a run, be that by trying to kill the Johnson, making off with whatever they asked you to steal, or any other way, I would ask that you discuss it with the other players at the table. If everyone agrees to the derailment, then by all means go for it. I will do my best to adapt as situations come up.
The Sixth World is dark, dangerous and doesn't give a solitary drek about you. Of course, there are pockets of light and goodness that keep everyone going. My goal in running Shadowrun is to give both the light and the dark. Most jobs will probably be dark, because Shadowrunners are, for the most part, doing bad things in order to continue paying rent. However some of my runs will either have the explicit goal, or give the opportunity for, feel good moments. When it comes to running jobs, I want the players to do their cool stuff, so if you have an idea that is a little out there, but it might be cool, feel free to bring it to the table and I will do my best to make it work with you.
When I run Shadowrun, this is the one thing that I want to make the most clear. Actions have consequences. Messing around gets you messed up. People who offer you jobs expect you to be professionals, and while you might not always do things the way they like, if it gets done reasonably, everything is good. If you sabotage the job, or turn on the Johnson, or just play silly bugger games, then word of what you do is going to get out and it's going to negatively affect you. If you taunt the Street Sam who got hired to work security to the point where he's going to hold a grudge, expect that to come back to bite you.