I understand that you don’t want to undermine the ROTJ ending (and that’s something I’ve struggled with as well), but I’m not sure that Mothma is the right character to make that happen. Ignoring her lack of screen time for a second, one of her defining traits is that she was part of the Rebellion from the beginning. She basically founded the beta version of the Rebellion in ROTS, and her biggest role was as the leader of the entire organization in Rogue One. I doubt that she would be an Imperial agent all along, given how long she’s been there.
The problem, then, is who should be the leader of the Rebellion? Maybe it could be some disgruntled Imperial leader, pissed that the Rebellion won so easily, and trying to rebuild the Empire to be stronger than before. Picture Moff Gideon from Mando, just with much more power and resources.
Well the formation of the rebellion in ROTS didn’t make the cut, so I’d place that in the canon alongside other such deleted scenes that don’t necessarily qualify canon-wise (ie Luke and Leia’s extremely romantic moments in the TESB medical centre or the conversations between Jedi in the prequels that were reshot in another locations). And I’m discounting Rogue One because obviously in my scenario RO would have been considered in the overall plan re Mothma. So my canon version is the 6 original movies as they appeared in the cinemas. In that canon she’s simply the nice lady in ROTJ who announces the Death Star stuff. But you might be right in stating there’s just too much overall lore surrounding Mothma (outside of the 6 films) to make it convincing.