He was afraid of Miraak.

Clavicus Vile mentions the Dovahkiin is close to his level in strength. Alduin mentions even Daedra fear him.

Something about Dragons puts them on a similar level to Daedric Princes, the Dragonborn has the soul of a Dragon. It isn't too far fetched to assume that Hermaeus Mora didn't want to risk directly engaging Miraak until you had weakened him, and simply used that angle to manipulate himself a new servant and gain the Skaal secrets.