I don't see the plot hole at all, I just see you wanting there to be one?

Haldath was, as was stated, completely in control of himself when he possessed the eyes. Nidhogg then fled to his brother because he was gravely wounded. How could he both consume/become Haldath and maintain his other form?

Secondly, while the eye you used was weakened, the other was still strong. In a moment of foolish confidence (Estinien's flaw), he lowered his guard -- as we were warned of several times -- and was consumed by the power that he claimed he mastered. This was foreshadowed for several quests, so where are you getting that it comes out of nowhere?

I don't think we were supposed to take Estinien as being at the zenith of his dragonphobia then, though. It seems he was actually somewhat stayed in his animosity as he bids Iceheart farewell following her sacrifice. It's more likely that he just thought "his watch had ended," and in that moment the Elderseer's warning came true.