When going for clean hands run, I found sneaking around the guards as opposed to taking them out more efficient anyway
I try that when I can, but even then it seems like there are open spaces where no matter where you skulk/hide, a guard will see you if you make a move to a spot you need to get to.
Or I might just suck at stealth.
Either or.
Part of the trick with Emily is to use the other abilities and gimmicks to distract guards and pull them out of their position, and then you can take them down.