Pardon me for being facetious, but this is what I'm hearing.
Player: I want to stealth into the Imperal base, slit the guard's throat, pick the lock to get in, find the computer room, and slice the mainframe all while being silent.
GM: Sounds good. Roll a hard stealth check.
Player rolls stealth check: OK... Two successes and one advantage.
GM: Excellent. Even though the moon was bright and the guards were on a steady patrol you were able to move without being seen.
Player: Since I was silent, do I get advantages on the attack on the guard?
GM: Actually, I wasn't done talking. Now, where was I. You're moving silently. The chrome on your blade glints in the moonlight, but the guard never saw it. Your blade slices through his flesh and he falls. You're able to catch the body before it hits the floor and makes noise. You creep up to the door and with a flourish of fingers on the keypad, the door slides open with a muffled woosh. It takes a few moments for your eyes to adjust to the lights inside. Once inside you skulk through the halls, keeping low out of sight from windows and ducking past open doors and hallways. Towards the back of the building you find the computer room, just where your blueprints showed. Since it's after hours theres no one in the room so you can enter without alerting anyone else in the building because you're moving quietly. Your fingers work across the keyboard with a deft ease that reduces the typical hard clack from typing fast. You're able to find the data you're looking for and download it into your datapad.
Player: All that from a single stealth roll?
GM: Yup. We're playing a narative game. You were quiet and it would be lame to have you roll a combat , skulduggery, and computer checks. If you failed those your being quiet wouldn't be awesome. Since you passed the stealth check, and were doing everything silently, you did everything. We're following the rule of cool, my friend.
Personally, I feel that a second check is in order when someone wants to do a stealth kill. I'm perfectly fine with it being a hit = kill and miss = damage. I'm also fine with it being a normal combat check, because it shouldn't be too hard for a trained person to kill a single minion, a crit on a vibroknife is only 2 advantages. Heck, I'm also fine with spending a Triumph on a stealth roll achieve the stealth kill. I agree that the concept of wounds breaks down when doing something that should be an auto kill, so doing something to make the stealth kill easier than a normal combat roll isn't out of line.
I just don't see combining two (or more) different skills into a single roll just because rolling dice could break the story the GM is telling. In fact, the dice should be helping to tell the story. Get advantages on the stealth check? Get some boost dice on the attack because the guard is distracted. Get threat? Get some setback dice because the guard thought he heard something but isn't looking your way yet. The dice are used to help tell the story, they don't get in the way of the story.