Taking down Gisarmory before the guards show up would probably skip them. That's all right, though- it makes sense, as Gisarmory would be unable to call reinforcements after being shut down.
I'll have a few minor edits to the dialogue next patch addressing both points.
Yep, the orange enemy should respawn. It's just orange to show it's tougher than usual- a few enemy groups later will do this as well.