This is RWBY there are a lot of abandoned towns and villages. I very much doubt Salem ordered the destruction of every single one of them. It's probably just the Grimm reacting to negative emotions. As for him alerting the Grimm, that can be explained away as him being a survivor of his town/village's destruction. And as for fixing up the Turrets, anyone with knowledge and education on how they work should be able to do it, it's not exactly a game changer.
Don't you think your making Salem out to be too all seeing and all knowing here, I mean if she has that kind of information gathering power then she would have won the game a long time ago, so if she does have it then there's got to be some serious limits to it. In fact the only information gathering Grimm we've seen so far are the Seers.
Even if that's true the SI has no way of knowing nor have enough evidence to come to that conclusion so it irrelevant.
Think of Salem's large scale command of the Grim as something like an RTS player, and her general awareness of them as something like a mental minimap, fog of war and fields of 'vision' a.k.a grim senses, included, with her Seers serving as camera drones to give her an actual personal eye view of things.
Admittedly, her setup's probably more nuanced and personalised than that, but she's an evil immortal sorceress Queen who's had literal centuries to optimise her command over creatures she shares an inherent connection with due to her taking a dip in the substance that made them.
If she didn't have at least this level of awareness of them after that long she'd be incompetent, and thus already sealed away by this point.
Given that she isn't? Yeah, she's at least got some equivalent of RTS-style awareness of her Grim, with the similarities to said genre being a simple matter of human ergonomics.
All this said, if you're playing an RTS and suddenly an enemy appears on your minimap in an area that should be clear? Then either said unit has teleported itself or
been teleported, or they've managed to stealth around your units long enough to either arrive there undetected or survive since the last time said spot was contested ground.
It doesn't matter which answer it is, because either way it points to said unit being
special due to either teleportation capability, someone
using said ability to transport them, exceptional stealth, or exceptional camouflage.
Three of these four explanations are potentially enemy action, all four of them are also potentially opportunities, and at least two of them are guaranteed to provide additional intelligence regarding what has happened.
It's a fairly obvious move to have someone investigate, along with backup in case it's a trap, which the reactivation of the turrets would make decent bait for, like one of those "your forces are under attack" messages, though mostly just notable due to it happening somewhere it shouldn't be, not to mention the odds of a random surviving villager being someone with the technical knowledge to fix said turrets is kinda low, further raising the odds of it being a trap
"So, you're a blacksmith?"
"Yes."
"And also a computer technician good enough to get around the safety lockouts in those turrets programs, and automate their operation?"
"Yes?"
"Doubtful, I think we're done here. Tell my Husband 'Hi' for me the next time I kill him, would you? Thanks." And then there were teeth and claws.... everywhere.
Yeah, I really don't think the 'surviving villager' scenario is heading Salem's most likely list, here.
Aside from that though, the bit about her having won already is dependant on her objective being the extinction of humanity, instead of say, screwing over Ozpin and remoulding Human- and Faunus-kind in her image, or any number of other likely objectives given her almost certain ability to just cut a lap around a kingdom's territory and have all the grim within it charge toward said settlement.
Chances are that if she did so she could just walk in after them and cut down any points of resistance, and even if she was driven off at that point the Kingdoms casualties would stunt them long enough for her to mass another attack and finish things.
It's pretty much how she operates in canon in volume 7, though in said canon her objective list has been explicitly stated as gain relics and maiden powers, crush Ozpin's forces, then rule Remnant as it's dark Queen, so chances are she's there to conquer, though I'll admit her goals might be different in this fic, even if said changes wouldn't have an effect on the scope of her command of the Grim.
And as for the MC 'not having enough evidence to come to that conclusion?' Absence of proof is not proof of absence, and someone dumped in a literal death world with outside context knowledge of it isn't going to go "Well, there's no
proof Salem's minions are here to kill me due to her sensing my arrival, even if I've watched the show enough to realise she'd probably keep an eye out for anomaly's due to being dicked over by the gods... repeatedly....."
No, odds are it'd have been one of those niggling concerns in the back of his head while he was stuck in the village and teching up, Summer standing between himself and possible proof of it's validity once he sees her tangling with Tyrian on his proverbial doorstep.
In a situation like that, acting to eliminate such an immediate future concern is pretty much common sense if one's presented with an opportunity, which he was.
"Tyrian was a potentially a threat, unlike Summer, so I dealt with him."
"Really, how so?"
"I converted him into a Holey Man."
Because yet again, the burden of proof of them not being there to kill him rests on Salem's side in this case, otherwise why
wouldn't our SI kill off the crazed zealot assassin who might be out for his blood, If only to prevent him from trying to kill him later if not sooner. Especially since Tyrian meeting Summer there would mean Salem's side would probably case the scene for anything significant if they won.
Anything else would be depending on them being arbitrarily disinterested in their job or our SI being better at hiding than they are finding, and I'm pretty sure Beowolves have enhanced normal senses to go with their empathic ones, at least if the Ursa's reaction to that red tree sap was anything to go by....