Maybe. But we only heard the official story, gained by torture from the various members of the Angelodulist sect, who each have their own view perspective. Also the Synod is a place for theological discussion, right? So maybe Sophia could be persuaded (or "persuaded") to renounce those of her doctrines which are most sticking out, in exchange for pardon (+some honorary post or other small concession from the official faith).
The Synod would be such a place for theological debate, but the Lightbringer has been very forward in gaining followers and has amassed a private army in the Anatolia Coast and Aepygtus. She may be too powerful and too zealous to reason with. We may invite her lieutenants to the synod to advocate their reforms on her behalf, but the Lightbringer herself is likely too far gone. Even if her beliefs are declared orthodox, by seizing power and passing laws, she has infringed on the rights of the Emperor and the Senate, which she will need to be called account for.