Well of course there are two ways to do magic in a subtle manner, do magic that no one can notice, or do magic that can have another explanation.
Say I make a spot on the floor slippery through theurgy, whose to say that I didn’t prepare that in advance? If I make arrows hit the vulnerable places on a target, whose to say the archer just didn’t get lucky?
Now, theurgy seems to be a blood powered force magic, dealing with manipulation of matter and energy so far, and of course this is going to be limited by the native’s understanding of matter and energy. I figure there will be no destroying cities by magically making nukes in this game. 
Something that isn’t clear to me is the possibility of making permanent alterations.
Even with those limitations, we could deepen shadows and muffle sound to enhance stealth, make people sick by manipulating their stomach contents, add a coating to weapons, make arrows and other projectiles strike true, make floors slippery, perform ventriloquism, and make melee attacks miss off the top of my head.
If we can make permanent alterations, or at least alterations that last a while, the PC could go all science hero with their transformation abilities, making explosives, accelerants, paralytics, poisons, drugs, irritants, and other chemical concoctions for example. Limited to of course what chemicals are known, but with the nature of theurgy chemistry might be pretty advanced.