Usually when I steal, I do exactly what you do, ie. make sure no NPC has a clear line-of-sight when I execute my action. So far, I haven't encountered the situation you described (but then, since you're playing TotSC, it may not matter). Maybe you can try casting Invisibility (it lasts 24 hrs and doesn't wear off 'easily', unlike 'hiding in shadows') before you act?
For my case, when filching the Bastard Sword +3 against Shapeshifters, I just sent 2 guys (one with the Boots of Speed) inside, picked the lock and swiped the sword (you can pause when the chest inventory sub-screen is open!), before making my way out. Of course, I placed the slower-moving guy at the exit before I did the deed so I would have a clear exit. The guards would stay in the house; they would not not come out (nor appear in the next house) and chase you (unlike in BG2). End of story.
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