In Better Call Saul it is clear that Gus wants Nacho dead, dead before he can be forced to talk to the Salamancas. Why not simply have him killed when he opened the gate to Lalo's hacienda? The very fact that the cartel knows that Nacho is a rat means that someone is behind him and certainly Gus is one such possible someone.
Is this a case of the writer not having thought of this at the time?
Had Gus ordered the mercenaries to kill Nacho in Lalo's compound, then the Cartel and the Salamancas would primarily suspect Gus of being the mastermind of the assassination. Lalo had been trying to mess with Gus' operation throughout most of Season 5 (the Cartel, through Juan Bolsa knows about this) and there is known bad blood between Gus and the Salamancas since Lalo's uncle, Hector Salamanca murdered Gus' close friend, Max.
Gus wanted to blame the assassination on a Peruvian cartel, and set Nacho up as the rat. Had Nacho been killed by the mercenaries in Lalo's compound, then that would clear him of suspicion of being a rat.
Gus had Mike plant bank transfer documents and the telephone number of the motel where Nacho is, in Nacho's safe. The bank transfer documents suggest that Nacho was on the payroll of a Peruvian cartel ("Los Odios, out of Peru").
Gus' original plan was then to lead the Cartel/Salamancas to Nacho's location (through the planted documents in the safe), and then have Nacho die in the ensuing gunfight. To force Nacho into a gunfight, he was given a gun, was instructed to not leave his room and to shoot anyone that walked in. Gus also had hired someone to make sure Nacho doesn't leave. Gus just didn't count on Nacho being smart enough to figure out that he's being set up.
Within the story, it’s risky for the mercenaries to “go loud” and kill someone unnecessarily —- especially someone who’s alerted to their presence and might fight back —- when they should be maintaining stealth as long as possible. It’s also risky to delegate killing one of your “team” to other members of that team. (If you were a mercenary, would you trust an employer who ordered you to kill someone else who works for him?)
Above the story, it’s hard to “juggle” multiple story beats at once. This scene was already the intersection of “Nacho betrays the cartel in a way he can’t come back from” and “Lalo survives an attempt on his life.” Fitting “Nacho is betrayed by the same man he became a traitor for” (and its sidecar, “Mike becomes further alienated from Fring because their codes do not align”) into the same scene would be one convolution too far.
