Since Cissnei is raised by Shinra in their orphanage facility, she possesses a high level of loyalty to the company. As stated in her in-game profile in Before Crisis:
“Her loyalty to the Shinra Company and the Turks in particular is unquestionable. Having been raised by them, she came to realize throughout the years that, while the company has done some questionable things, they have also brought ease and progress to the lives of countless people. For better or for worse, she'll stick by them."10
During Zack and Cloud's escape from the Shinra Mansion, when Cissnei first found Zack at the shore, she was torn between duty and friendship. Even though she chose to remain loyal to Shinra and the Turks, she showed some hesitance before attacking Zack. Although she was defeated by Zack and was told not to follow him or he would attack her for real, she still acted as a member of the Turks carrying out her mission and pursued Zack.
In the second encounter with Zack and Cloud on the same night, Cissnei noticed Cloud was in poor shape, after Zack explains that Cloud's condition was due to Mako poisoning, Cissnei drew her own conclusions as to how Zack and Cloud was treated as Hojo's test subjects.
Perhaps due to her being a Turks member and having been influenced by the likes of Tseng, Reno and Rude, Cissnei ultimately chose morals over duty, telling Tseng that she has lost the targets and letting Zack and Cloud escape.