I think the question presents an interesting quandary for the series. The games have shown Riku to be capable of redeeming himself for his actions in KH1 and the majority of his arc is spent learning how to make amends and let go of his guilt over his own darkness in order to better command it so that it can never be used for evil again. Axel manipulated Roxas and Xion over the course of Days by deliberately withholding information and working behind their backs; he enabled the involuntary isolation of Namine within Castle Oblivion at least for a time and, like Saix, he kidnapped Kairi to serve his own ends, but he's back as full-fledged hero of light with his own Keyblade by the end of DDD. Terra allowed himself to be manipulated through his own desire for power at any cost, and his unwillingness to subject his actions to the scrutiny of others out of pure hubris led to many of the tragic events which preface Sora's journey in KH3; yet he is shown in Blank Points to be wiser to Xehanort's schemes and prepared to resist his influence inside of his heart. Ansem the Wise was a bigot who felt he could use other beings he saw as unfit for existence to whatever ends he so desired in order to enact his own personal revenge: in these endeavors he was not a victim of untoward influence or manipulation, and yet he too has made strides towards redemption characterized by an acknowledgment of his own wrongdoings and a vocal desire to set things right.
Our problem as an audience is that we know so much less about Isa, about what is driving his opposition to the light and what really instigated his alliance with Xehanort. I don't believe that his actions have been driven by the "seed" within his heart and it's my feeling that he made the choice to side with Xehanort because he, like many other characters within this series, is flawed and susceptible to the darker side of his own heart, which pretty much everyone has to contend with (except for characters with little to no development like Disney princesses and Kairi). Even Sora falls victim to it: driven to indiscriminate rage in Chain of Memories over false memories he doesn't pause to reconsider (and what does that say about Namine, who was so lonely and yearning for connection that she put those false memories there and collaborated in the Organization's plan to capture Sora with full knowledge of what she was doing), and then felled in DDD when he can't see how vulnerable he really is and thinks he can carry the pain of others by himself.
I like Isa because there is a symbolic duality to his arc. He challenges Axel repeatedly to reaffirm the importance of their friendship when he knows it's threatened by the never ending, labyrinthine machinations of Xemnas and Xigbar (which he himself is party to). He calls Xion a puppet and seems to regard her with either indifference or contempt yet he musters up a defense for her (albeit coded in his usual objectifying language) when Xigbar recommends she be eliminated early on for abandoning the Organization.
I think there would be dramatic value to having Isa perish at the hands of Lea or another major character with close ties to him. But I think the series could get even more mileage out of exploring what it is that Isa is afraid of losing (a central theme of Days and a factor in all of the major Organization characters' arcs) and how that has driven him to act in such a duplicitous fashion. Personally, I think that Isa feels betrayed, abandoned and used-- used by Lea for a convenient friendship until he was simply replaced by Roxas and Xion, used by Xehanort and ultimately losing his original existence as a result of that. Perhaps in siding with Xehanort he is seeking a semblance of control or at least of power over his own destiny; in that sense, I believe he is redeemable and I believe he can be "saved," but for him that may not look like a completely happy ending.
In the end, my view is that nobody really dies in Kingdom Hearts. Every heart goes through the washing machine and is born anew, so maybe for Isa a proper ending is a renewal so he has a chance to start with a clean slate and live the life he didn't have a chance to enjoy this time around.