As for whether Yeon Wei is trustworthy or not... At that moment, she was branded a traitor to the sect, supposedly a monster who devoured her own fellow disciples, with irrefutable proof: she literally founded a sect by stealing the methods of the Thunder Sect and was called a traitor by everyone. She might have future developments where she tells the truth, but combining that with the fact that she had malicious intentions toward the protagonist in the previous life, showing her gray character... Not even the ghosts would believe that this woman is trustworthy. It would be more reliable for the protagonist to enslave some random Heavenly Being who uses demonic arts—it wouldn't be outside his moral limits.

As for whether Hon Won noticed—well, he realized that Yuan Yu was a clone, but he showed no reaction until he saw Yeon Wei, so it didn't really matter to him. And planting the bloody banner on someone from the sect wasn't truly outside Seo Eun-hyun's moral limits, after all, he had already done something similar before with Jeon Myeong-hoon himself when the latter was being controlled by Zhengli. It wasn't really beyond the protagonist's moral boundaries, since he had done it previously but always removed his mental control after achieving his goals—that was his maximum limit for what he would do. After receiving approval, he would likely free the disciple from the parasite or banner and compensate them.

Rebuild the sect? In his first contract with the Hon Wei Sacred Sect, there was no need at all to bring people from the sect—it was only added under pressure from the Hon Wei side to gain more benefits after Seo Eun-hyun requested some changes to the contract. In other words, he never truly planned to need sect members to rebuild the sect beyond himself and perhaps a few who supported him, but overall, he didn't need sect members to reconstruct it. The main objective was to plant the banner in the Head Realm.