It really depends on how one individually defines "evil" and from what viewpoint you look.
For the "good" guys, like Sora, Roxas, Kairi, Riku or Mickey Saix was clearly one of the "evil" guys, in the way he acted and behaved he was clearly an asshole and utterly ruthless, although that may hold true for the whole Organization since they were threatening world order and abusing other people and their hearts.
Nonetheless, specifically for Saix, and most likely by extension Isa, he is probably the most evil one after Xemnas and Xigbar himself since he has not only the Xehanort-eyes and ears but also was the most loyal to Xemnas in KH2.
After Axel chose to care for Roxas and Xion and refused to place the original plan he had with Saix over them it seemed Saix abandoned it altogether and sided with Xemnas fully.
As for Isa's allegiance now...who knows? I wouldn't be surprised though if he were now Xehanort's second "right hand man" beside Braig.
@rac7d:
Gosh, can you write in an understandable manner please? It's very strenuous to decipher that. 0_o