Your sure there isn't an issue with being detected? Like you have a mod that turns off the detected message?
But anyways ... the script that makes npc's react to the player when they mouse over with weapon drawn is hard coded to a special topic.
"PLAYERINIRONSITES"
So no way to alter that script ... But a game setting maybe ???
And it does look like you can attach additional conditions to each response under this topic per quest it was added to. So a reference condition of the player , IsSneaking with is not equal ( != 1 ) might work.
You'll have to look up the dialogue for any particular npc's you want to change this on. So after you bring up their dialogue ... select the topic of "PLAYERINIRONSITES" and notice what quest the responses reside in. Then open that quest and bring up that topic again. Select each response and add that condition. This should effect every npc that calls to that quest.
Hope that helps ... but check out game settings too.