Indeed, 3rd is about the lowest level I'd want to start a thief-centric campaign at. A bit of hand-waving about "intensive training" or, alternately, a "life spent on the streets" and you have your justification.
On the subject of one-blow knockouts, of course guards can have any number of hit points the DM wants them to have... suppose the novice characters' first targets are guarded only by cheap mercenaries (who are cheap because they're kinda wimpy = below average hp)? Maybe these are targets that aren't really worth the time of higher-level thieves, but the Keepers might see them as perfect "in the field" training opportunities for certain up-and-comers.
Or for more training opportunities, perhaps the Keepers set up "dummy" target locations with happy employees who are well paid to collapse convincingly the first time they are coshed with a sap? These mock guards would role-play (!!) real guards, and behave accordingly... except that they are using blunted swords and arrows that cause subdual damage. This one may require a little DM chicanery if the players aren't aware it's just an exercise (and we don't want the characters killing off these helpful hirelings, either; one kill and that'd be the end of that idea as far as the rest were concerned).
Check into alternate hit point systems (VP/WP, Ken Hood's Grim-n-Gritty, others?); one of these *might* make things easier.
(MILD SPOILERS for Thief/Thief II)
The Keepers always struck me as non-thieves... more like loremasters. Can't recall why. I only recall inferring they were pulling Garrett's strings because he could pull off stunts they couldn't. Certainly they wanted to prevent the NPCs in Thief (I) from doing what they ended up doing, but for some reason they didn't take direct action... they dumped Garrett into it.
And oh yeah, for more low-magic flavor, make sure the undead are as fearsome as they are in the computer game... maybe like low-HD trolls, they have regeneration against all but fire and holy water (acts like acid against them). If the PCs have access to other energy types, those might work too (DM's discretion as always).
The payload on a water arrow will also douse "robot" boilers (the larger models take two shots in quick succession -- the first cools the boiler sufficiently that the robot is momentarily immobilized, but he warms right back up in 1 or 2 rounds). I'd say the robots launch bombs that are equivalent to mines, except they explode a moment after landing (often scattering 5-10' in the interim). Robots may have to wait until the PCs have a few more levels.
(END SPOILERS)
With the moss arrows providing a circumstance bonus to Move Silently, remember to throw in circumstance penalties for noisy floors (metal and tile especially). A moss arrow ought to cancel any such circumstance penalty.
Ahem. Well, what can I say, I've been replaying Thief II recently.