It depends on how you make the rig. If I make an articulated fly now, I'm more inclined to use a barbless treble hook rather than a two hook rig. I also use the articulated shanks that are now available or if I can't get them I use the pre-made wires that are used in making flutter jigs, which are a lot cheaper than the shanks made specifically for fly fishing. When I first started making articulated flies. I would cut the front hook off at the bend, heat it and make an open "loop" that I could slide through the eye of the back hook squeeze the loop close and then wrap it.
I think it's a pretty low risk that the hook would end up in the gills of the fish. I can't remember it every happening even when I was fishing jointed lures which might have two or three treble hooks on them.
Here's one of my first attempts at an articulated fly. It was tied for pike. Front is a hook shank cut at the bend with a 4/0 Partridge Pike used for the articulated portion.

Jointed Pike Fly 1.jpg