The short reason was that we wanted CE to be a technical showcase of everything up to that point. When Geiger made that Temporal Flux teaser back in 2004, which teased the idea of having Toma and Schala in your party, having a different party member because a killer innovation. Since the 8th character wasn't feasible, and since we knew replacing any member with Schala would offend the dearest fans of that party member, human Glenn was the best way to do this.
But yeah, it was just going to be explained that thanks to the conciliatory nature of everything after CT (and based on Magil replying that Glenn, in fact, wasn't his enemy in Radical Dreamers by being silent on the topic), the thrust would be that Magus lifted the spell.