It's one of the trade-offs of using those kinds of weapons so you'll want to either stun-and-sneak-away or stun and hide the body. I just ALWAYS hide the body in case there's some patrolling NPC I haven't accounted for, or if I mess up later and accidentally lead some guys from another room into a self-made opium den.
This is the first game where I feel like hiding the body matters. Like I said, though, in this case I thought I had cleared the patrol, not realizing that a few guys were close enough to the alarm to come running in just after I jumped down from the vent.
At this point in the game any interest in Ghost is gone and I'm used to running around with alarms going off, paying no attention to them because anyone within hearing distance is dead or unconscious.