Rule 1 of hacking high security nodes: Don't be seen.
Rule 2 of hacking high security nodes: If you are seen, don't stick around to play with the elite spider.
Rule 3 of hacking high security nodes: A good biofeedback filter is your friend.
Rule 4 of hacking high security nodes: Do your legwork to find out what kind of IC is used and plan accordingly.
Really, is this so much worse than a spider using Black Hammer? Being dead makes you far less able to perform your role than a negative quality.
Paying karma is not the only way to remove the quality, as you would know if you'd actually read the section of Unwired that deals with psychotropic program options. Regardless, however, this is no different from the corpsec tossing a grenade down the cramped hallway to catch the team in the chunky salsa effect. Shadowrun is not meant to be sweetness and light. Corpsec guards use lethal force all the time, and actively try to kill the characters to the best of their ability, using actual tactics. And there are times when a team member will go down in the middle of a run, and be unable to fulfill their part of the plan. What do you do then? Do you just give up and go home? Or do you overcome, adapt?
Do me a favor, and reread both the program options and the program as I described it. If the hacker is getting hit with this, they're already either going to be getting knocked out altogether, or going to have to use cybercombat to dump the spider so he can jack out before reinforcements arrive. By the time this thing's going off, the time for hacking is over, and the time for getting out of the system before your brain is fried is here. If they were using Black Hammer, instead of Blackout, you'd be DEAD, not simply unconscious.
No plan survives contact with the enemy. Sometimes, that plan falling to pieces leaves a team member incapable of doing their job, because 'sucking chest wound' tends to interfere with, say, casting spells, driving, or aiming your gun, and so the team has to adapt as they get the hell out of dodge. This is no different. Would you cry foul if the group didn't do proper legwork before assaulting a MCT zero zone, and found out the hard way that there was monowire strung between certain plants in the courtyard, or that some of the 'flowers' sprayed your toxic gas of choice?
And if they play it well, you might reward them with some extra karma, and perhaps getting a contact of theirs to hook them up with some time in a PAB unit to get that quality erased without paying the karma (for a bit of nuyen, of course), or even the Mr. Johnson, if they were professional about the job.