This one is a pain in the neck. I seem to remember doing this on the "Gotham PD" level, which has been frozen over by Mr. Freeze.
The strategy I used was to knock everyone out except for the guy wearing the scrambler backpack (since taking him out last is one of the other challenges). Then, throw a sonic batarang into one of the two large side rooms that have railings over the doorways.
After he heads into the room, stand on the railing above the open doorway. When the thug is finished investigating the batarang and heads back out towards the center area, you can do the inverted ledge takedown on him.
This guy doesn't use my strategy (although he manages to do it quite a bit quicker) but you can watch him get the takedown here: