My issue is, it's because of her leadership this has happen and hurt the mages even more. She has hurt the very people she was fighting for in more ways then one.
Both sides have been hurt in the war, we can already see that Templars have lost much of the respect they used to get from people too. Blaming the leaders is something inevitable that often happens but that doesn't make it any less wrong. People, mages followed her because they wanted to, no one forced the rebel mages to stay with her, they could always remain with loyalists. You have to consider the fact that all Libertarians and most Aequitarians joined the rebellion, the remaining mages had a choice.
Fiona wanted autonomy to begin with, the amount of resistance she faced was unimaginable so she had two choices, to surrender or improvise. She chose the latter.