I mean, they've seen him fight (for example, the confrontation with the press gang on the surface). I can definitely follow the "better safe than sorry" reasoning but I hope you can also see why "default to lethal force" is not necessarily a pattern we want our bodyguards to have long-term.
They've seen him fight. They've seen him bleed. They can still smell the blood on him. They tortured him almost to death as a test of faith. They know, better than others, that while he's hardier than normal people, he's still mortal.
So a naval officer with a sword is still a credible lethal threat.
Remember, they didn't kill the guy for making threats. Or for drawing his weapon.
They killed him for threatening to kill Ignatius while drawing a weapon. Not counting any hidden weapons he might have.
After all, the last Inquisitor that almost killed Ignatius before Imperial intervention used a hideout pistol.
There's several teams of naval ratings here armed with shotguns and the like. None of them have been shot.
It's not like the Sisters were shooting civilians in a crowd that attempted to crowd Ignatius either.
If we don't want them to kill someone, we give them explicit orders.
But their current RoE seems entirely reasonable.
