I have used it, sometimes on friends, but usually against enemy necromancers. My most common conjuration is a Dremora Lord, though I sometimes use Atronachs. When I come across a powerful mage, who can be more dangerous to the enemy (read: Keep my sorry Adam-55 alive longer) then I do whatever must be done. As someone else said, when you're trying to kill me, you give me the green light.
I have actually thralled a dead follower though. Eric got killed in the college battle over the Eye of Magnus. He never disappeared, and I could drag him to the door but not through it. I tried everything I could to get him out of there. When I got the thrall spells, I took dead thrall too. I thralled him and walked him back to Rorikstead, where I put him back in his Blades armor and "buried" him on the peak overlooking his town.
Best I could do under the circumstances. It's not always a bad thing, just like war.