Give this a try...
“Colour to Alpha” is fantastic in some cases, not so much in others. I’ve seen the same issues as you have when using it. The images you were trying to cut out sort of becomes “ghosted” I guess. I think it’s because “colour to alpha” effects the whole canvas, not just certain sections.
You have the option of masking out the standard white background by using the fuzzy selection tool and using then “quick mask” (control+q to toggle between editing modes). Anything that comes up in red will be kept safe from editing (duh- it’s a mask hehe), anything surrounding this can then be changed. However, I just took that method for a test drive, and while it works, I didn’t personally like it too much. It still left a slight white halo issue, which is not what you want if you plan on pasting it to a new "scene".
I’m going to try and explain a way to get rid of the halo in The GIMP… it works well… but I have never seen a tutorial for it for GIMPers… so if this is hard to follow- I make apologies in advance! Photoshop does something similar, so I take no credit, this is just translating it for GIMP users.
- Take your snapshot of the model on the standard white background.
- Open it up in The GIMP.
- Grab the “fuzzy selection tool”.
(My settings for the fuzzy selection tool are anti-aliasing checked, Threshold 15.0 and select by composite.)
- Make a selection somewhere in the white background area.
- Go to Select >>> Invert (or keyboard shortcut Control+I)
- Then go to Select >>> Shrink and shrink the selection by 1px with “shrink from image border” checked.
- Now go to Select >>> Float… and create a new layer from the floating section via the layers tab.
- You should now have two layers. The top one is the one you’ll want to add in to your “scene”, the lower layer, or the old background, will be white with the halo “residue”.
This method isn’t bullet-proof, especially around area’s with a lot of transparency (alpha hair textures are a fab example of when it doesn’t work the best). But if you combine both “colour to alpha” with the “shrink and float” method, once you get used to it… you will save a LOT of time!
Let me know if that works.

(Or if i need to review the instructions to make more sense- lol).