The zombies in thief 2... there really are no places you really have to mess with zombies... You can bypass all of them... Most won't even awaken unless you purposely get close to them (graveyard zombies)... There is little in the graveyard you need to get out of those tombs... Even still you can pick up stuff without even waking the zombies...
You don't even have to release the zombies in the necromancer's tower, and if you do, they are so easy to run away from.
I really can't see how zombies in the second game could destroy the atmosphere... or get in the way of it... You could probably play through the game, without even encountering them at all... That is to say you have to be going out of your way to even run into them.
The main exception is the undead hammer haunts (not counting the ghost one), that are awake and moving about, but those exist in only two fairly remote and limited spaces. They can't chase you out of those places, and are relatively easy to avoid if you stick to the shadows. You'll experience your first 'haunt' (non-threatening IIRC, ghost one in a secret dungeon in 3rd level, it'll chase after noises), you'll encounter a dangerous physical one in the fifth level in underground crypt, IIRC (when you go the mechanist seminary).
Hammer haunts are like mechanists/hammerites that can't die, running on adrenaline... You can't knock them out with the blackjack... They are destroyable though, IIRC. Take them out with one hit with a backstab with the sword, or damaged by sword fighting in general (not recommended). But basically just an uber guard with a skull-face skin.
Likewise they are somewhat similar to the guards with the facemasks or neck armor, that you can't knock out with your blackjack... But you can use gas...
These things shouldn't be enough to pull you out of the 'thievery' "realism"!
BTW, you can encounter zombies in the third level of Thief 2, but they are not easy to get to, and if you get to them, there is no way back the main map. They are there as an easter egg.
Hmm according to the thief wiki, apparently there is another zombie in Truart's house in unpatched version of Thief2, but doesn't appear in teh patched version (1.18 patch)...?
http://thief.wikia.com/wiki/Zombie It also says that zombies appear in the unpatched "Life of the Party', however, zombies also appear in the patched version as well (only if you read the scroll in the necromancer's tower). So I'm not sure what the Wikia's context is exactly.