Currently there is no way to remove a skin from autoskinner. A situation happened where a user wanted to have 2 weapons of different skins, but keep the auto skin for everything else (keep autoskinner enabled). He also uses all the presets, so making a new one is not an option.
Possible idea:
When the "Allow Owned Skins" is set to false, the default skin shows up as an option. Could this be an option at all times, and if selected, then this would "disable" the item from the autoskinner?