First off, your player is being disruptive, and is flat-out wrong. The book is very explicit that glitches are not supposed to be "life-ending" by any measure. Even a critical glitch only "puts the character's life at risk" and doesn't immediately end it... Tell them to re-read the second paragraph under the Glitches header on page 45.
Second, there are actually three possible ways to get a glitch. Successful glitch, a failed gltch, and a critical glitch. Many people overlook the fact that failing a test while glitching is not the same thing as a critical glitch. Critical glitches only occur when you get enough 1's to glitch while also not getting any successes. Glitching on an attack where you simply don't get more hits than the defender (but still got a hit or two) is just a regular glitch, not a critical one.
1. The argument that the glitch penalized the players (even potentially) is fallacious. You made a ruling about what the glitch meant (ganger blew off watch duty and turned his back to take a leak). The players then chose to shoot him while he was still next to the edge of the building. At that point it is on them, they could have chosen to sneak past him entirely, or waited until he was away from the edge, or evendors moved in for a melee attack. The player is being sore, and trying to blame you for the group's failure at foresight. Bullets cause knockdown, true story.
2. This is a great example of a glitch, and is reflected in the specific rules for glitching on an extended test. Make sure to check out those rules if you haven't already.
3. Personally, I would suggest doing different things with glitches each time (not every glitch is the same), but saying that a glitch negates the effect of the called shot is good. It gives a bit of a penalty without negating the entire attack. The missed attack has a couple aspects to it, though. I mention above that it is possible to miss, glitch, and not critical. If I read your situation right, I think this might be what happened. In which case, spending the edge negated the glitch entirely.