I just went though this and the answer is yes. Just make sure you get it deep enough, either IM or Sub Q as per your vets instructions. I always lift up on the needle just a bit to make sure it's under before I inject. If you do this and you can see the needle, you'll be under the shed and not into the snake. I'm assuming you've seen a shed before so you know how thin it really is. Trust your experience and proceed as normal. Speedy recovery!
Dave