The impact of Werner Ziegler's murder upon Mike Ehrmantraut suggests that Nacho Varga will be allowed to live in characters not in Breaking Bad. While viewers know where the likes of Mike, Jimmy McGill, and Gustavo Fring will end up, if not the exact whys and hows, the fates of Nacho, Lalo Salamanca, and Kim Wheeler in particular are all uncertain and, in some cases, cause for concern.
While much of that is regarding Kim's future and whatever potentially dire end awaits her, the same can be said for Nacho. The character is effectively Better Call Saul's version of Jesse Pinkman at this point: a low-level criminal who has a good heart, dragged into schemes and rivalries so much bigger than him. By the end of Better Call Saul season 5, Nacho is caught in the firing line as tensions escalate between Gus and the Salamancas. Botching the job to kill Lalo, it leaves him stuck between an Albuquerque rock and a Mexican hard place; Lalo will want to kill him for revenge, and Gus may want to in order to clear up loose ends connecting back to him.
If Gus does decide to kill Nacho - which, again, feels like an obvious choice for him right now - then it would fall to Mike to be the executioner. That's a role Mike has played in both Better Call Saul and Mike killed Werner on Gus' orders in Better Call Saul season 4, because Lalo was investigating him and there was a risk of Fring being exposed. Mike, even the consummate professional killer, got the job done, but it's changed something within him, as seen in season 5, and that could continue in season 6.
In one particularly telling Better Call Saul season 5 scene, Mike had a postcard of the Sydney Opera House taken down from a bar wall, because it reminded him of Werner (whose father was the engineer behind the iconic structure). It was clear that the guilt of killing Werner was weighing incredibly heavily upon Mike's shoulders, affecting him in a way most of his murders before and after did not. That shift continued throughout Better Call Saul season 5. While for the most part it's arguable he was the same Mike viewers have long known, there were moments where he'd stand-up to Gus or try to push back on things. Most notably, after learning that Gus had been using Nacho's father against him, Mike told his boss that "fear [isn't] a great motivator," wisdom Gus later repeats in Breaking Bad.
It's clea that killing Werner has had a real impact on Mike, because he had to kill someone who was largely innocent. Nacho is more involved in the criminal underworld, but still wouldn't deserve the grim fate that may await him. With Mike increasingly of this view and looking to not only protect Nacho, but perhaps make amends for what happened with Werner, then convincing Gus not to kill him, or otherwise finding a way to help Nacho escape, could be a fitting way of him squaring things in Better Call Saul season 6.