Can we use the Scythe to get into Vanduul-controlled space? EG sneak past a few guards or the likes?

Flying a Scythe is step one, but there will be more to sneaking behind enemy lines than just having an alien ship. You'll need to do more work (having the proper codes, IFF signal, etc.) in order to safely transit Vanduul space. It's certainly the first part of the equation, though!