Rowan understood that although in the greater schemes of things, the Reflections were weak. Like him, they had grand roots, but the circumstances they found themselves in were incredibly poor, it would have to be, because they were the survivors of a Primordial onslaught, it was a miracle that they existed at all.
Despite all this, killing the Reflections came with consequences that he was willing to accept, the alternatives could not be considered. One of the consequences was his haunting by the Eye, and to suppress this unwanted affliction, he had to seal the Eye, at least until he became strong enough to decipher all its secrets.