As a GM who just got done sniping the group's combat mage in the head with a gel round, I can say that the sniper thing can be a very effective tool to let the player know that they done pissed someone off. You don't even have to kill the character, just slam a 9P AP -2 sniper rifle round with standard aiming/smartgun bonuses into them and let the dice fall where they fall. Needless to say, that mage probably won't be stunballing a SWAT team for no reason again...
Another trick is for the PCs to just get picked up by the opposition with sweeper teams. Drug their booze, have them get narcojetted while they're taking a dump, sap them into submission while they wait for a taxi or any other nefarious, underhanded technique to get them caught. The characters wake up in a room strapped to chairs and the corp goons go to working them over while video taping the whole thing. Characters released, the video dumped in YouTube with a warning that it would have been cheaper and easier to kill them and the corp wins out in the end with face saved and stock prices going back up after the last fiasco.
Well, the runners have a problem with their reps for a while but that just makes things interesting...