Well, you can always drop her out of the BG1 -> BG2 transition and you'll get the vanilla BG2 Imoen. Well, it's not entirely vanilla if you use the Level 1 NPCs or other mods, but still...IS it a good idea to dual imoen this late?
Also, is it possible to get her potrait switched to her BG2 one?
If that's not the optimal solution, you can use the ShadowKeeper to make a few adjustments, or the console... yes that's cheating.
For example you can dual her to a mage in the game and then set her enough XP to level her up to the 11th level mage to get the Thief abilities back, and then reduce the XP back to zero or close and not use the mage side for a while if you don't feel like it.
The portrait is easy to edit with the ShadowKeeper too.
Hmm, what would you say about dualing her at 9 and keeping her there giving her a +1 int tome?