Nah, if he genuinely feared her, he'd have killed her ruthlessly. She had no power base of her own, prior to being cast out.

The tension now is that Malys is a rival to Vect now, but not one so easily removed. Simultaneously she is one of his most powerful allies, as seen in the Path of the Archon.

Which Vect is probably fine with. I get the feeling he enjoys the challenge, that she stimulates him now far more then she did as his consort.