my vet does sedation as a standard procedure. We had our Freya euthanized last year. First step was to put in an IV. Then sedation shot. Then after she was drowsy, the "final" shot. They checked her to make sure that she was "out" before giving the final dose.
My vet explained it that NOT doing the sedation is cheap and, in his opinion, cruel. When the agent hits the blood stream to stop the heart, the natural body response is one of panic. He likened it to being awake while drowning vs dying in your sleep. The cost of the sedation drug is tiny compared to a comfortable death for the animal and the peace of mind of the owner.
I'm so sorry that you had to witness that. Honestly, I'd go back and give the vet a piece of my mind.