Search-Fu didn´t work and i am too lazy to look more properly. So again: what do you think about social skills during combat? Negative modifiers and workable or "no chance"? I am not talking about "hey, go kill yourself", but of a simple "STOP, let us talk" - (so that my fellow runners can sneak up behind you while you are confused). Any suggestions?

are you looking for RAW or house rules ?

there's leadership tests and intimidation,

Commanding voice does what you want I think as an almost guaranteed,

but, for a mundane running up to the BBEG yelling "wait, please let us convince you to not be Evil" ... sorry but it just doesn't work that way,

ME? I'm probably more likely to kill you for trying Chummer ! but if you roleplay it well, your GM should at least give you a chance, as long as you are shouting from cover

like in a true negotiation scenario

RAW-wise I would think you'd get the "NPC's attitude toward character" and "character's desired result" penalties to the roll, which would probably start at -6 dice minimum but could easily go to -10 or worse. Commanding Voice (adept) and Control Thoughts (magician) will both give you at least a chance, but you have to have natural line of sight on every target you want to use them on, so no doing that while you're hiding behind cover. Hope your magic-user is a troll.

If I were the GM I probably just wouldn't allow it, mostly because I don't like the idea of ignoring logic for the sake of dice rolls. You have to think that at least one guard would guess a runner team's "sudden change of heart" halfway through shooting the place up was a trick, no matter how hard they're sweet-talked. At the very least, I would make it so that it would be a huge disadvantage to the PCs for them to try this - make them disarm first, position the guards so that it's impossible to sneak up on them without an invisiblity spell, blast the PCs with Stick-n-Shock as soon as they step out of cover ("you want to talk? you can talk in the interrogation room") or whatever. If it gets to the point that there's a flat-out firefight, the NPCs have no reason to trust the PCs and should act accordingly.

Having said all that, this is assuming that the PCs are obviously runners and the NPCs have no reason to think they'd just stop fighting. If the PCs could spin it as a friendly-fire incident (assuming they have the right disguises), or if the guards opened fire first and the PCs never actually fought back (and it wasn't a zero-zone), then yeah, I'd allow that.

Using social skills in combat all comes down to your tactics.

There are a few examples on how to use social skills/tricks in combat in Style Over Substance (link in sig.) though I'll probably add some more.

Rulewise, you'll have a high negative modifier due to your relationship with the characters on the other side of the fight. But you can get positive modifiers to counter this: many people don't want to risk getting killed in combat, and offering a peaceful resolution can get you a positive modifier for offering an outcome that's beneficial to the target. Having a reputation as someone you can talk with can help with people who are aware of that reputation.

Intimidation can also be used to get the opponent to run away, or to stop shooting, especially if you've got the upper hand in the fight - or look like you have it (style over substance, once again). You can also try to make people believe you're on their side, or pretend to be badly hurt/feign death, or enrage your enemies so that they make tactical mistakes...

Of course, you can get them to stop shooting, but this doesn't necessarily mean they'll agree to talk it out. They can just try to get you to drop your gun so that they can shoot you without any risk. And if you Intimidate them so that they run away, they can still call for backup or prepare a trap for you in the next room.

There are also volume issues to contend with, guns are loud. I'd go so far as to apply the -2 Interfering Sound penalty from the Perception Modifier table. (SR4a, pg. 136) If a player tried this stunt while the bullets were already flying this is how I'd handle it.

At the bare minimum I'd apply the following Modifiers to the PC's DP:
With respect to the character, the NPC is: Hostile -3
Subject is distracted -1
Interfering Sound -2 (Perception Penalty)

& the following Modifiers to the NPC's DP:
Subject is distracted -1

Everything else would depend upon the tack that the PC takes, they will be fighting an up-hill battle of words no matter how they slice it.