Yup. This was a wasted opportunity in BG2EE, frankly.
They should have gone the Mass Effect 2 way, with the Paragon option being to save the "paladin" Samara, and the Renegade option to save the "assassin" Morinth (SPOILERS, I guess?).
For the same reason, I think Clara should be a Good aligned character. Not only because a single class Good Thief is long overdue, but also because there is no indication that she has some extra talent, other than that. Sure, she is listed as Evil, but that's because she's "representing" Hexxat, at the moment.
She has NO personality, while under Hexxat's "spell".
After she is freed, her personality might be a little more intriguing than the boring zombie she is in the game.
As for the kit... no reason to make her anything else than a regular Thief. Same for the special abilities: if you can come up with something cool and fitting... sure. But nobody ever said that she has to be AS STRONG as Hexxat. Actually, plot-wise, it would make much more sense if she was weaker (she is saved and gets to be free only with YOUR help).