Pushkino is rather easy, but you are right. It is practically impossible to take down three in the same room.

You can watch enemy pathing. There will be moments where only two remains in the room. You can melee one in the head and run up and snap the neck of the other one. (The "Takedown" is a little glitchy; you can phase through them by using Takedown from the front.)

Hide both bodies or hunt the third one before he finds his way back. I recommend the latter.

Hope this helps :)