It's good for story telling if you want to go there.
I'm playing a low level scientist yet again and definitely planning to use the cloning machine in some not so good ways this time around. There was a recent cowplant thread and my clones are going to make me potions for awhile. At least in the first testing phase. I'm already setting it up. Usually though the clones I make become workers for the scientist. Workers is a nice way of putting it.. I have in the past gotten rid of the evil clones .. except the clone of my scientist. Now I'm playing evil sims more so ehh we'll see where the story goes.
The clone mimic interactions are great to me also you need to look at those.
If you want to get rid of them but can't work it any other way you can always just delete the "mistakes" in managed worlds.