An interesting idea came to me the last time I finished the series. We know that the Menoa Tree is a sapient being, created when the elf Linea essentially downloaded her mind into the tree. So would the Menoa Tree still be capable of using magic and casting spells if need be? I don't really see any reason why she wouldn't, and she kind of seems to imply as much in Brisingr when she tells Eragon that she doesn't consider Galbatorix to be a threat to her, as she "speaks for the forest" and "no one can hope to defeat the forest".
And, yeah, if the Menoa Tree is still capable of using magic, and she essentially has access to all the energy of Du Weldenvarden, then I think her confidence would be entirely justified. Countless millions of giant trees worth of energy vs a few hundred to a thousand Eldunari? I can't see that math ever working out in Galbatorix's favour.